GIAO NMR Research Articles

Iriomoteolide-1a and -1b: Structure Elucidation by Integrating NMR Spectroscopic Analysis, Theoretical Calculation, and Total Synthesis.

The structure of iriomoteolide-1a, a marine macrolide with potent cytotoxic activity against human cancer cells, has been under scrutiny for more than a decade since the first total synthesis of the proposed structure was achieved by Horne. Here we disclose the correct structure of iriomoteolide-1a. Given a huge number of possible stereoisomers, we adopted an integrated strategy toward the structure elucidation of iriomoteolide-1a: (1) NMR spectroscopic analysis/molecular mechanics-based conformational analysis for configurational reassignment of the macrolactone domain; (2) model synthesis for validating the reassigned configuration of the macrolactone domain; (3) GIAO NMR calculation/DP4+ analysis of side chain stereoisomers; and (4) total synthesis of the most likely structure. Moreover, the correct structure of iriomoteolide-1b, a natural congener, was also determined by an integration of NMR spectroscopic analysis, GIAO NMR calculation/DP4+ analysis, and total synthesis.

Cytotoxic diterpenoids from Croton kongensis inhibiting tumor proliferation and migration

Thirty-two diterpenoids including 18 ent-kauranes (1–6, and 12–23), nine 8,9-seco-ent-kauranes (7–8, and 24–30), four ent-abietanes (9–10, and 31–32), and one crotofolane (11) were isolated from the twigs and leaves of Croton kongensis. The structures of previously unreported crokokaugenoids A–H (1–8), crokoabiegenoids A–B (9–10), and crokocrotogenoid A (11) were determined by spectroscopic data analyses, TDDFT-ECD and GIAO NMR calculations, and X-ray crystallographic studies. All compounds were evaluated for their cytotoxic activity against five human tumor cell lines, and the structure–activity relationships were discussed. Biological tests exhibited that compound 1 possessed strong anti-proliferation activity, arrested cell cycle at G2/M phase, and induced cell apoptosis of MDA-MB-231. The mechanism investigation showed that compound 1 can inhibit tumor proliferation and migration by targeting mitochondria to increase intracellular reactive oxygen species (ROS) and regulating STAT3 and FAK signal pathways. Collectively, these findings supported the great potential of compound 1 as a hopeful anticancer agent.

Phytochemical and biological studies on rare and endangered plants endemic to China. Part XXXVI. Tsugaforrestiacids A–O: Structurally diverse C-18 carboxylated diterpenoids from the twigs and needles of the ‘vulnerable’ conifer Tsuga forrestii and their inhibitory effects on ATP-citrate lyase

An extensive phytochemical investigation on the EtOAc-soluble fraction of the 90% MeOH extract from the twigs and needles of the ‘vulnerable’ Chinese endemic conifer Tsuga forrestii (Forrest's hemlock) led to the isolation and characterization of 50 structurally diverse diterpenoids, including 15 unreported C-18 carboxylated ones (tsugaforrestiacids A−O, 1−15, resp.). Among them, compounds 1−7 are abieten-18-oic acids, compound 8 is an abieten-18-succinate, and compounds 10−12 are podocarpen-18-oic acids, whereas compounds 13−15 are pimarane-type, isopimarane-type, and totarane-type diterpenoid acids, respectively. Their structures and absolute configurations were determined by a combination of spectroscopic methods, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism (ECD) data, and single crystal X-ray diffraction analyses. All the isolates were evaluated for their inhibitory activities against the ATP-citrate lyase (ACL), a key enzyme in cellular metabolism. Tsugaforrestiacids E (5) and H (8) were found to have significant inhibitory effects against ACL, with IC50 values of 5.3 and 6.2 μM, respectively. The interactions of the bioactive molecules with the ACL enzyme were examined by molecular docking studies. The isolated diterpenoids also provide chemotaxonomic evidence to support the delimitation of Tsuga from its closest sister group (Nothotsuga). The above findings highlight the importance of protecting plant species with unique and diverse secondary metabolites, which may be potential sources of new therapeutic agents for the treating ACL-associated diseases.

Undescribed polyketides from endophytes associated with the critically endangered conifer Abies beshanzuensis

Four undescribed polyketides, beshanzones A (1) and B (2) as well as beshanhexanols A (3) and B (4), along with three known ones (5–7) were isolated from the rice fermentation of two endophytic fungi associated with the critically endangered Chinese endemic conifer Abies beshanzuensis. γ-Butyrolactone derivatives 1, 2, and 5 were isolated from Phomopsis sp. BSZ-AZ-2, an interesting strain that drawn our attention this time. The cyclohexanol derivatives 3, 4, 6, and 7 were obtained during a follow-up investigation on Penicillium commune BSZ-P-4-1. The chemical structures including absolute configurations of compounds 1–4 were determined by spectroscopic methods, Mo2(OAc)4 induced electronic circular dichroism (IECD), GIAO NMR calculations and DP4+ probability analyses. In particular, compound 2 contains a novel 5/5 bicyclic ring system, which might be biogenetically derived from the known compound 5 through hydrolysis followed by an Aldol reaction. All isolates were evaluated for their antimicrobial activities against a small panel of bacterial and fungal pathogens. Compounds 6 and 7 showed moderate inhibitory activities against Candida albicans, with MIC values of 16 and 32 μg/mL, respectively.

A new canthinone glycoside isolated from the root barks of Ailanthus altissima with NO inhibitory activity

One new canthinone glycoside (1), together with six known compounds (2–7) including three lignans (2–4), two coumarins (5–6) and one phenol (7) was isolated from the root barks of Ailanthus altissima. The structure of new compound 1 was established by the interpretation of UV, IR, MS and NMR data, while its absolute configuration was determined by acid hydrolysis and GIAO NMR calculations with DP4+ probability analysis. The inhibitory effects of all compounds on Nitric oxide (NO) production were investigated in lipopolysaccharide (LPS)-induced RAW 264.7 cells. Results showed that compounds 2 and 5 displayed NO production inhibitory activity with IC50 values of 30.1 and 15.3 μM, respectively.

Holotrichones A and B, potent anti-leukemic lindenane-type sesquiterpene trimers with unprecedented complex carbon skeletons from a rare Chloranthus species

Two lindenane-type sesquiterpene (LDS) trimers with unprecedented carbon skeletons, holotrichones A (1) and B (2), were obtained from the whole plant of Chloranthus holostegius var. trichoneurus by a ultra performance liquid chromatography-photodiode array detector-mass spectrometry (UPLC-PDA-MS)-guided isolation strategy. Compound 1 represents the first LDS trimer incorporating a unique 3/5/6/6-fused framework, in which a lindenane-type monomer and the 2-methylbutyryl substituent of an LDS dimer is bridged by a six-membered ring system. Compound 2 is the first hetero-trimer fused by an LDS dimer with a p-benzoquinone-meroterpenoid, featuring an unusual 3/5/6/6/3/5/6/6/6 nonacyclic system fused by the sesquiterpenoid unit and a 2-geranyl-6-methyl-2,5-cyclohexadien-1,4-dione moiety. In compound 2, the dimeric LDS moiety is equipped with a rare oxaspiro[4.5]decane system. Their structures, including absolute configurations, were established by spectroscopic methods, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism (ECD) calculations, and single-crystal X-ray diffraction analysis. The plausible biogenetic pathway speculation indicated that hetero- and homo-Diels-Alder additions may dominate the formation of these highly fused polycyclic frameworks. Both compounds 1 and 2 induced the human acute myeloid leukemia MV-4–11 cell death via apoptosis induction, which deserves further investigation on this new chemical class of LDS oligomers for their anti-leukemic potential.

Phytochemical profiling of Striga asiatica; characterisation and anti-microbial assessment of the isolates

One undescribed compound, striasinol (1), and twelve previously described compounds were isolated from the aerial parts of Striga asiatica. Structure elucidation of isolated compounds was achieved by the interpretation of 1D and 2D NMR and HRESIMS data. The absolute configuration (1S,5S) of 1 was ascertained based on GIAO NMR calculations, DP4+ probability analysis, and a comparison of the experimental and calculated specific rotation values. The isolated compounds were evaluated for their antimalarial action, and none was found to be effective against the chloroquine-sensitive (D6) or chloroquine-resistant (W2) strains of Plasmodium falciparum. The isolates were found non-toxic to the Vero cell line as well. Subsequent testing of these metabolites for antimicrobial activities against various bacterial and fungal strains (up to 20 µg/mL), revealed that compounds 6 (chryseriol) and 7 (apigenin) showed a reasonable activity towards methicillin-resistant Staphylococcus aureus ATCC 1708 (MRSA), with IC50 values of 5.81 and 3.60 μg/mL, respectively.

Quinoline, Indole, and Isogranatanine Alkaloids from Malayan Leuconotis eugeniifolia.

Nine new alkaloids, eugeniinalines A-H (1-8) and (+)-eburnamenine N-oxide (9), comprising one quinoline, six indole, and two isogranatanine alkaloids, were isolated from the stem-bark extract of the Malayan Leuconotis eugeniifolia. The structures and absolute configurations of these alkaloids were established based on the analysis of the spectroscopic data, GIAO NMR calculations, DP4+ probability analysis, TDDFT-ECD method, and X-ray diffraction analysis. Eugeniinaline A (1) represents a new pentacyclic quinoline alkaloid with a 6/6/5/6/7 ring system. Eugeniinaline G (7) and its seco-derivative, eugeniinaline H (8), were the first isogranatanine alkaloids isolated as natural products. The known alkaloids leucolusine (10) and melokhanine A (11) were found to be the same compound, based on comparison of the spectroscopic data of both compounds, with the absolute configuration of (7R, 20R, 21S). Eugeniinalines A and G (1 and 7) showed cytotoxic activity against the HT-29 cancer cell line with IC50 values of 7.1 and 7.2 μM, respectively.

Impacts of basis sets, solvent models, and NMR methods on the accuracy of 1H and 13C chemical shift calculations for biaryls: a DFT study

Introduction: Biaryls are core structures composed of chiral ligands, organocatalysts, biologically active natural products and biopolymer lignins. In this study, the effects of basis sets, solvent models, and NMR methods on the accuracy of 1H/13C NMR chemical shift calculations for biaryl structures were evaluated. Methods: All calculations were performed using Gaussian09. The GIAO NMR results were observed and extracted using GaussView05. To reduce the systematic error of the calculations, linear regression analysis of the calculated chemical shifts versus the experimental shifts was performed. Results: The tested basis sets showed good 1H/13C results, with CMAE values as low as 0.0425 ppm and 1.09 ppm for 1H and 13C, respectively. The use of solvent models significantly increased the accuracy of the 1H chemical shift calculations. The GIAO method produced more accurate results than did the IGAIM and CSGT methods. Conclusion: This study recommends 6-31G(d,p) and DGDZVP basis sets, IEMPCM and CPCM solvent models, and GIAO NMR methods for the accurate prediction of 1H and 13C chemical shifts for biaryls, assisting in their full structural assignments.

Chippiine, iboga, cleavamine, vobasine, and cytotoxic bisindole alkaloids from Tabernaemontana polyneura

Eight undescribed indole alkaloids, polyneurines I–P (1−8), comprising one chippiine, two iboga, one cleavamine, three vobasine, and one vobasinyl-iboga bisindole alkaloid, were isolated from the bark of Tabernaemontana polyneura. The structures of these undescribed alkaloids were established by interpretation of the MS and NMR data, while the configurations were determined using GIAO NMR calculations and DP4+ probability analysis, and TDDFT-ECD method. Polyneurines I (1) and J (2) are characterized by the presence of an additional pyrrolidine ring incorporated within the chippiine or seco-coronaridine skeletal framework. Biosynthetic pathways towards the formation of polyneurines I (1) and J (2) are proposed. Polyneurine P (8), along with four known bisindoles, showed appreciable cytotoxicity against HT-29, HCT 116, MDA-MB-231, and A549 cancer cell lines with IC50 values ranging between 0.3 and 9.0 μM. The variation in alkaloidal content observed between the present and previous study, both involving the same plant species but occurring at different locations, is also discussed.

Structurally Diverse Metabolites from the Marine-Derived Streptomyces sp. DS-27 Based on Two Different Culture Conditions.

Nine new compounds, including streptothiomycin A-E (1-5), two cyclopentenones (6, 7), one α-pyrone (8), wailupemycin Q (20), along with sixteen known compounds were identified from a rhizosphere strain Streptomyces sp. DS-27 derived from the marine cordgrass Spartina alterniflora under two different culture conditions. All of the structures were elucidated by extensive analysis of 1D/2D NMR and HR-ESI-MS data. The absolute configurations were determined by NOESY analysis, ECD, specific rotation and GIAO NMR calculations, and DP4+ probability analysis. Bioactivity investigation showed that compounds 5 and 7 exhibited significant inhibitory effects on LPS-induced NO production in a dose-dependent manner, which indicates their anti-inflammatory potential.

Nocaviogua A and B: two lipolanthines from root-nodule-associated Nocardia sp.

Nocaviogua A (1) and B (2), two lipolanthines featuring a non-canonical avionin (Avi)-containing macrocycle and a long acyl chain, were identified from the mutualistic actinomycete Nocardia sp. XZ19_369, which was isolated from the nodules of sea buckthorn collected in Tibet. Their planar structures were elucidated via extensive analyses of 1D and 2D NMR, as well as HRMS data. The absolute configurations were fully elucidated by advanced Marfey's analysis and GIAO NMR calculations, representing the first time that the configurations of this family of lipolanthines have been determined. Nocaviogua A (1) exhibited weak cytotoxicity against human chronic uveal melanoma cells (UM92-1), non-small cell lung cancer (NCI-H2170), and breast cancer (MDA-MB-231). Our work provides valuable information on this burgeoning class of lipolanthines for further investigations.

An ECD and NMR/DP4+ Computational Pipeline for Structure Revision and Elucidation of Diphenazine-Based Natural Products.

Discovery and structure elucidation of natural products available in infinitesimally small quantities are recognized challenge. This challenge is epitomized by the diphenazine class of molecules that contain three bridged stereocenters, several conformations, ring fusions, and multiple spatially isolated phenols. Because empirical NMR and spatial analyses using ROESY/NOESY were unsuccessful in tackling these challenges, we developed a computational pipeline to determine the relative and absolute configurations and phenol positions of diphenazines as inhibitors of eukaryotic translation initiation factor 4E (eIF4E) protein-protein interactions. In this pipeline, we incorporated ECD and GIAO NMR calculations coupled with a DP4+ probability measure, enabling the structure revision of phenazinolin D (4), izumiphenazine A (5), and baraphenazine G (7) and the structure characterization of two new diphenazines, baraphenazine H (3) and izumiphenazine E (6). Importantly, through these efforts, we demonstrate the feasibility of NMR/DP4+ analysis for the determination of phenol positions in phenazine-based molecules, further expanding the limits of computational methods for the structure elucidation of complex natural products.

Squamabietenols A–F, undescribed abietane-O-abietane dimeric diterpenoids from the ornamental conifer Juniperus squamata and their ATP-citrate lyase inhibitory activities

Six undescribed naturally occurring abietane-O-abietane dimers (squamabietenols A–F) together with one 3,4-seco-totarane-type, a pimarane-type, and 17 related known mono-/dimeric diterpenoids were isolated and characterized from the needles and twigs of the ornamental conifer Juniperus squamata. The undescribed structures and their absolute configurations were established by extensive spectroscopic methods, GIAO NMR calculations with DP4+ probability analyses, and ECD calculations. Squamabietenols A and B showed significant inhibitory effects against ATP-citrate lyase (ACL, a novel drug target for hyperlipidemia and other metabolic disorders), with IC50 values of 8.82 and 4.49 μM, respectively. A molecular docking study corroborated the findings by highlighting the interactions between the bioactive compounds and the ACL enzyme (binding affinities: −7.1 to −9.0 kcal/mol). The unique abietane-O-abietane dimeric diterpenoids are quite rare in the vegetable kingdom, and they are of chemotaxonomic significance for the Cupressaceae family.

Structure Elucidation of Two Intriguing Neo-Debromoaplysiatoxin Derivatives from Marine Cyanobacterium Lyngbya sp. Showing Strong Inhibition of Kv1.5 Potassium Channel and Differential Cytotoxicity

Two aplysiatoxin derivatives, neo-debromoaplysiatoxin I (1) and neo-debromoaplysiatoxin J (2), were isolated from marine cyanobacterium Lyngbya sp. collected from the South China Sea. Their structures including absolute configurations were assigned by spectroscopic analysis, in combination with GIAO NMR shift calculation and DP4+ analysis. Structures of neo-debromoaplysiatoxin I and neo-debromoaplysiatoxin J contained a decahydro-5H-pyrano [2,3,4-de] chromen-5-one 6/6/6 ring skeleton and an intriguing peroxide bridge group, respectively, which are unprecedented structure scaffold and motif in aplysiatoxins. Two compounds displayed comparable inhibitory activities against Kv1.5 K+ channel with IC50 values of 2.59 ± 0.37 μM (1) and 1.64 ± 0.15 μM (2); however, they presented differential cytotoxic effects. It is worth noting that neo-debromoaplysiatoxin J, containing a peroxide bridge, showed remarkable cytotoxicity against four cancer cell lines including SW480, SGC7901, LoVo and PC-9 compared to the human normal cell line.

Eugeniifoline, a Pentacyclic Indole Alkaloid from Leuconotis eugeniifolia, and Configurational Revision of Synthetic Eugeniifoline Isolated from a Diversity-Enhanced Extract.

Eugeniifoline (1), a pentacyclic indole alkaloid with a five-membered ring E, was isolated for the first time as a natural product from the stem-bark extract of Leuconotis eugeniifolia. Eugeniifoline (1) was previously reported as a synthetic product from a diversity-enhanced extract, but with the configuration at C-21 reported as S (1a). The configuration at C-21 was revised to R as shown in 1, based on the NOE data, GIAO NMR calculations, and DP4+ probability analysis, as well as the TDDFT-ECD method.

Polyneurines A−H, iboga alkaloids from Tabernaemontana polyneura

Eight undescribed iboga alkaloids, polyneurines A−H, were isolated from the bark of Tabernaemontana polyneura. The structures of these alkaloids were established by interpretation of the MS and NMR data, while the configurations were determined using GIAO NMR calculations and DP4+ probability analysis, TDDFT-ECD method, or X-ray diffraction analysis. Polyneurine A possesses a γ-lactone unit embedded within the iboga skeleton, while polyneurines D and E incorporate a formylmethyl moiety at C-3 of the iboga skeleton. Biosynthetic pathways towards the formation of polyneurines A, C, D, and E were proposed.

Polyoxygenated Terpenoids and Polyketides from the Roots of Flueggea virosa and Their Inhibitory Effect against SARS-CoV-2-Induced Inflammation

Six new polyoxygenated terpenoids, podovirosanes A-F (1-6), and two known polyketides (7 and 8) were isolated from the roots of F. virosa. Their structures, along with absolute configurations, were deduced using spectroscopic analysis as well as computational calculations, including TDDFT calculation of ECD spectra and GIAO NMR calculations combined with DP4+ probability analysis. Compounds 2, 3, 5, and 8 were found to reduce the phosphorylation levels of NF-κB p65 in SARS-CoV-2 pseudovirus-stimulated PMA-differentiated THP-1 cells.

GIAO NMR Calculation-Driven Stereochemical Assignment of Marine Macrolide Natural Products: Assessment of the Performance of DP4 and DP4+ Analyses and Assignment of the Relative Configuration of Leptolyngbyalide A–C/Oscillariolide Macrolactone

Abstract The stereochemical assignment of marine macrolide natural products by quantum chemical calculations is often hampered by the generation of an intractable number of conformers in molecular mechanics conformation searches. In this study, we assessed in detail the application of GIAO NMR chemical shift calculation and DP4-type statistical analyses to the stereochemical assignment of two marine macrolide natural products, whose relative configurations had been incorrectly assigned in the originally proposed structures. We also examined how DP4+ probability was affected by cumulative Boltzmann population level of molecular mechanics-derived conformers. Finally, GIAO NMR chemical shift calculation/DP4-type statistical analysis was applied to leptolyngbyalide A–C/oscillariolide macrolactone, whose relative configuration has not been assigned so far.

Structure and Antimicrobial Activity of Rare Lactone Lipids from the Sooty Mold (Scorias spongiosa).

Two new lactone lipids, scoriosin (1) and its methyl ester (2), with a rare furylidene ring joined to a tetrahydrofurandione ring, were isolated from Scorias spongiosa, commonly referred to as sooty mold. The planar structure of these compounds was assigned by 1D and 2D NMR. The conformational analysis of these molecules was undertaken to evaluate the relative and absolute configuration through GIAO NMR chemical shift analysis and ECD calculation. In addition to the potent antimicrobial activities, compound 2 strongly potentiated the activity of amphotericin B against Cryptococcus neoformans, suggesting the potential utility of this compound in combination therapies for treating cryptococcal infections.