NOE Correlations Research Articles

Revisiting the Cyclocephagenols via Astragalus condensatus: Structural Insights and Configurational Revision.

The phytochemical investigation of the MeOH extract of Astragalus condensatus roots led to the discovery of a new tetrahydropyran cycloartane-type triterpenoid, astracondensatol A (1), alongside six known cyclocephagenol derivatives (2, 3, 20, 32, 35, and 36). Elucidation of their structures involved 1D and 2D-NMR spectroscopy and mass data analysis. Upon comparing NMR spectroscopic data with prior literature, several carbon shift anomalies, particularly at C-24, prompted a reevaluation using quantum chemical calculations, resulting in the revision of the 24S to 24R absolute configuration for compound 2 and 38 other reported cyclocephagenol-type triterpenoids. X-ray crystallography data further supported the analysis in establishing the absolute configuration of compound 2. Ambiguous NOE correlations and publication bias could have played a significant role in miss-assigning the C-24 absolute configuration in tetrahydropyran cycloartane-type triterpenoids.

Triantaspirols A-C and Paraphaeolactone Cs from Paraphaeosphaeria sp. KT4192: Sensitivity of CP3 in Distinguishing Close NMR Signals.

Hybridized spirobisnaphthalene derivatives, triantaspirols A-C (1-3) and paraphaeolactones C1 and C2 (4 and 5), were identified from the culture broth of the fungus Paraphaeosphaeria sp. KT4192. The NMR spectra of 2 and 3, as well as 4 and 5, closely resembled each other, indicating that these were pairs of diastereomers. Although this NMR spectral resemblance made it challenging to distinguish their relative configurations, detailed analysis of the electronic circular dichroism (ECD) spectra and NOE correlations allowed us to deduce them. The CP3 metric with the DFT-based NMR chemical shifts was found to distinguish configurations of diastereomers in a highly sensitive and accurate manner that DP4 could not account for because of the very close chemical shift differences in the experimental NMR spectra. The reliability of this method was assessed using 23 published examples which could not be distinguished by DP4 protocol.

Semisynthesis, Structure Elucidation and Anti-Mycobacterium marinum Activity of a Series of Marine-Derived 14-Membered Resorcylic Acid Lactones with Interesting Ketal Groups.

The incidence of Mycobacterium marinum infection is on the rise; however, the existing drug treatment cycle is lengthy and often requires multi-drug combination. Therefore, there is a need to develop new and effective anti-M. marinum drugs. Cochliomycin A, a 14-membered resorcylic acid lactone with an acetonide group at C-5' and C-6', exhibits a wide range of antimicrobial, antimalarial, and antifouling activities. To further explore the effect of this structural change at C-5' and C-6' on this compound's activity, we synthesized a series of compounds with a structure similar to that of cochliomycin A, bearing ketal groups at C-5' and C-6'. The R/S configuration of the diastereoisomer at C-13' was further determined through an NOE correlation analysis of CH3 or CH2 at the derivative C-13' position and the H-5' and H-6' by means of a 1D NOE experiment. Further comparative 1H NMR analysis of diastereoisomers showed the difference in the chemical shift (δ) value of the diastereoisomers. The synthetic compounds were screened for their anti-microbial activities in vitro. Compounds 15-24 and 28-35 demonstrated promising activity against M. marinum, with MIC90 values ranging from 70 to 90 μM, closely approaching the MIC90 of isoniazid. The preliminary structure-activity relationships showed that the ketal groups with aromatic rings at C-5' and C-6' could enhance the inhibition of M. marinum. Further study demonstrated that compounds 23, 24, 29, and 30 had significant inhibitory effects on M. marinum and addictive effects with isoniazid and rifampicin. Its effective properties make it an important clue for future drug development toward combatting M. marinum resistance.

Unveiling the anti-vitiligo, anti-inflammatory, and antitumor activities of sesquiterpene coumarins isolated from Ferula kuhistanica

Six undescribed bicyclic sesquiterpene coumarins, kuhistanin A, ferukrin isovalerate, 9’β,12’α - ferukrin isovalerate, (17′E)- 9’α, 12’β - isomarcandin, (17′Z)- 9’α, 12’β - isomarcandin and (17′E) - isomarcandin, together with nine known ones were isolated from the roots of Ferula kuhistanica Korovin. The structures of them were elucidated using NMR and HRESIMS data analysis. The relative configurations of the isolates were confirmed by NOE correlations and NMR calculation. The absolute configurations of them were confirmed by X-ray diffraction analysis and ECD calculation. Anti-vitiligo, anti-inflammatory and cytotoxicity of the isolates were tested. Acetyl feselol, feselol, ferusingensine I and farnesiferol A significantly increased the melanin content at the concentration of 10 μM. (17′E) - 9’α, 12’β - isomarcandin exhibited strong cytotoxicity against HT-29 cell line with IC50 values of 8.94 ± 0.47 μM, and (17′E) - isomarcandin demonstrated strong cytotoxicity against Hela, A549 and HT-29 cell lines with IC50 values of 5.29 ± 0.25, 4.01 ± 0.20, and 4.16 ± 0.21 μM, respectively. This study concluded that, isolated compounds from F. kuhistanica demonstrated strong bioactivity towards anti-vitiligo and cytotoxicity and active compounds are suggested as anti-vitiligo and cytotoxicity agent for future drug development.

Benzimidazolium bromide derivative inclusion complexes with native and modified beta-cyclodextrins

The interactions between four native and modified beta-cyclodextrins and a benzimidazolium bromide salt were analyzed through UV-Vis and NMR Spectroscopy. The new benzimidazolium salt was obtained by simple and efficient conversion of N-1 substituted 5,6-dimethylbenzimidazole with phenacyl bromide in acetone. In all cases, the complexes stoichiometry was 1:1, as determined from UV-Vis titrations. Based on the values for association constants, the strength of the interactions with benzimidazolium bromide was weakest with the methyl substituted beta-cyclodextrin and strongest with the sulfobutylether substituted beta-cyclodextrin. Through-space NOE experiments were used to investigate the structural aspects of inclusion process. The obtained NOE correlations indicate coexistence of two inclusion modes: one with the phenacyl group inside the cyclodextrin cavity and the second one with dimethyl-substituted benzene ring inside the cavity. The imidazole ring and the ethyl substituent have been proven to remain outside the cyclodextrin cavity in both inclusion modes.

Aaptocarbamates A−G, chlorinated terpene carbamates with antiosteoclastogenic activities from the marine sponge Aaptos sp.

Six undescribed chlorinated sesquiterpene carbamates, aaptocarbamates A–F, and a chlorinated tris-norsesquiterpene carbamate, aaptocarbamate G, were isolated from the marine sponge Aaptos sp. collected in Indonesia. Aaptocarbamates D–F and G possess tetrahydrofurans and a tetrahydrofuranone, respectively. The relative configurations of the tetrahydrofuran units were determined by the NOE correlations and DFT-based calculation of the 13C chemical shifts. This is the first time that chlorinated terpene carbamates have been reported from natural sources. Various aaptamine derivatives have been reported from the Aaptos sponges so far, the isolation of chlorinated terpene carbamates is very rare. Aaptocarbamates A, B, and D showed 60% inhibition of the RANKL-induced formation of multinucleated osteoclasts in RAW264 macrophages at 20 μM.

Cyclic Tetrapeptide Natural Product Asperterrestide A: Total Synthesis and Structural Revision

We have studied for the total synthesis of asperterrestide A, which is a cyclic tetrapeptide natural product reported to be composed of D-alanine, anthranilic acid, (2R,3S)-3-hydroxy-N-methylphenylalanine, and D-isoleucine or D-allo-isoleucine. We initially performed the total synthesis of the reported structure of asperterrestide A via solid-phase peptide synthesis and macrocyclization in solution. However, the spectral data of the synthetic (9R,25R)-derivative did not match those of the natural product. Then, we considered the true structure should be the (9S,25S)-stereoisomer because all NOE correlations predicted from its three-dimensional structures obtained by theoretical calculations were consistent with those observed in the natural product. Thus, the (9S,25S)-stereoisomer was synthesized through solution-phase synthesis because N-acylation of a polymer-supported (2S,3S)-3-hydroxy-N-methylphenylalanine derivative resulted in low yield. The (9S,25S)-stereoisomer was successfully synthesized and was found to be identical to the natural product. Therefore, the stereochemical configuration of asperterrestide A was corrected from (9R,25R) to (9S,25S). We also tested whether the DFT calculation of carbon chemical shifts can discriminate stereoisomers of cyclic tetrapeptides. After conformational analysis of four possible stereoisomers of asperterrestide A, Boltzmann-weighted carbon chemical shifts based on DFT calculations using Spartan’20 revealed a DP4 accuracy of 96%, which is sufficient to determine the stereochemical configuration among the stereoisomers. In addition, three 9-deoxy derivatives were synthesized and the cell growth inhibitory activity of the five synthetic compounds against human cancer cells (U937, MOLT-4, and A549) was evaluated. The results showed that the (9S,25S)-stereoisomer is as potent as asperterrestide A, whereas the (9R,25R)-derivative is not. The (9S,25S)-3-deoxy analogs were found to be equipotent to the natural product although the activity of the (9S,25R)-deoxy analog was lost.

Dactylides A-C, three new bioactive 22-membered macrolides produced by Dactylosporangium aurantiacum.

Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.

Genome-directed discovery of antiproliferative bafilomycins from a deepsea-derived Streptomyces samsunensis

Genomic bioinformatics analysis identified a bafilomycin biosynthetic gene cluster (named bfl) in the deepsea-derived S. samsunensis OUCT16-12, from which two new (1 and 2, named bafilomycins R and S) along with four known (3–6) bafilomycins were targetly obtained. The structure of 3 was clearly identified for the first time, thus named bafilomycin T herein. Differ from the fumarate substitution at C-21 of known bafilomycins, its location on C-23 is a unique feature of 1 and 2. The stereochemistry of the compounds was established based on NOE correlations, ketoreductase (KR)-types in PKS modules of bfl, and ECD calculations. Moreover, a detailed biosynthetic model of 1–6 in S. samsunensis OUCT16-12 was provided based on the gene function prediction and sequence identity. Compared with the positive control doxorubicin, 1–6 showed more potent antiproliferative activities against drug-resistant lung cancer cell line A549-Taxol, with IC50 values ranging from 0.07 μM to 1.79 μM, which arrested cell cycle in G0/G1 phase to hinder proliferation.

Thiocarbohydrazone and Chalcone-Derived 3,4-Dihydropyrimidinethione as Lipid Peroxidation and Soybean Lipoxygenase Inhibitors.

The potential of the 4,6-diphenyl-3,4-dihydropyrimidine-2(1H)-thione (abbreviated as KKII5) and (E)-N'-benzylidenehydrazinecarbothiohydrazide (abbreviated as DKI5) compounds as possible drug leads is investigated. KKII5 and DKI5 are synthesized in high yield of up to 97%. Their structure, binding in the active site of the LOX-1 enzyme, and their toxicity are studied via joint experimental and computational methodologies. Specifically, the structure assignment and conformational analysis were achieved by applying homonuclear and heteronuclear 2D nuclear magnetic resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and density functional theory (DFT). The obtained DFT lowest energy conformers were in agreement with the NOE correlations observed in the 2D-NOESY spectra. Additionally, docking and molecular dynamics simulations were performed to discover their ability to bind and remain stabile in the active site of the LOX-1 enzyme. These in silico experiments and DFT calculations indicated favorable binding for the enzyme under study. The strongest binding energy, -9.60 kcal/mol, was observed for dihydropyrimidinethione KKII5 in the active site of LOX-1. ADMET calculations showed that the two molecules lack major toxicities and could serve as possible drug leads. The redox potential of the active center of LOX-1 with the binding molecules was calculated via DFT methodology. The results showed a significantly smaller energy attachment of 2.8 eV with KKII5 binding in comparison to DKI5. Thus, KKII5 enhanced the ability of the active center to receive electrons compared to DKI5. This is related to the stronger binding interaction of KKII5 relative to that of DK15 to LOX-1. The two very potent LOX-1 inhibitors exerted IC50 19 μΜ (KKII5) and 22.5 μΜ (DKI5). Furthermore, they both strongly inhibit lipid peroxidation, namely, 98% for KKII5 and 94% for DKI5.

Cannabinoid-like meroterpenoids from Peperomia incana

Ten previously undescribed metabolites were isolated from Peperomia incana (Haw.) A. Dietr. (Piperaceae), among which four contained a chromene moiety, two were identified as meroterpene lactones, and four were cannabinoid-like compounds. While the chemical structures of the compounds were assigned based on HRESIMS and 1D and 2D-NMR spectra analyses, the relative and absolute configurations were assigned from NOE correlations and a combination of ECD data and X-ray single crystal analyses, respectively. In a cytotoxic assay against a panel of seven human cancer cell lines (A549, MDA-MB-231, HeLa, DU 145, 5637, Hep G2, and MIA PaCa-2, which represent non-small cell lung cancer, as well as breast, cervical, prostate, bladder, liver, and pancreas carcinomas, respectively) most of the isolated compounds showed promising cytotoxic activities. The incanachromenes B, and incanabinoids A and C exhibited the highest cytotoxicity toward all tested cancer cell lines with IC50 values in the range of 5.0–10.0 μM, whereas incanolides A, B, and incanabinoid B showed the lowest cytotoxic activity. In addition, incanachromene C and incanabinoid C produced a significant antibacterial effect toward planktonic cells and biofilms of multidrug-resistant Staphylococcus aureus strains.

Total synthesis of a reversed cyclopurpuracin using a combination of solid and solution phase methods

AbstractCyclopurpuracin is a cyclooctapeptide isolated from the methanol extract of Annona purpurea seeds with the following sequence cyclo‐Gly‐Phe‐Ile‐Gly‐Ser‐Pro‐Val‐Pro residue. In this study, a reversed cyclopurpuracin, namely cyclo‐Pro‐Val‐Pro‐Ser‐Gly‐Ile‐Phe‐Gly, was successfully synthesized using a combination of solid and solution phase synthesis methods. The precursor was head‐to‐tail cyclized using 1.25 mM in DCM with 3 eq. HBTU and 1% v/v DIPEA. The final product was obtained (3.8 mg) with an overall yield of 7.4%. The synthetic products were characterized by HR‐ToF‐MS, 1H‐NMR, 13C‐NMR, and 2D NMR, showing different NMR profiles. The presence of the conformation was confirmed by providing additional signals in the 1H NMR and 13C NMR spectrum and the correlation peaks shown by 2D NMR. The presence of the cis conformer in conformer B was proven by the chemical shifts of Ser6 Cβ, Pro7 Cβ, and Pro8 Cβ in conformer B, which were more upfield than the conformer A chemical shifts, and the presence of NOE correlation between Hα/Hα of Val7 and Pro8. The NMR of the reversed cyclopurpuracin revealed the presence of two conformers, conformer A (cyclo‐[trans‐Pro‐Val‐trans‐Pro‐Ser‐Gly‐Ile‐Phe‐Gly]) and conformer B (cyclo‐[cis‐Pro‐Val‐trans‐Pro‐Ser‐Gly‐Ile‐Phe‐Gly]). The presence of dual conformers has not been observed in the NMR spectra of natural cyclopurpuracin.

Cover Feature: The Extended Hadamard Transform: Sensitivity‐Enhanced NMR Experiments Among Labile and Non‐Labile 1Hs of SARS‐CoV‐2‐derived RNAs (ChemPhysChem 4/2022)

The Cover Feature illustrates how artifact-free 2D NOE correlations between labile protons can be obtained from an extended Hadamard encoding/decoding matrix, which supersedes problems in conventional Hadamard schemes. The sensitivity-enhancing abilities of extended Hadamard encoding operating in conjunction with solvent repolarization mechanisms are demonstrated on GHz NMR studies on SARS-CoV-2 RNA fragments. More information can be found in the Article by Lucio Frydman and co-workers.

Supramolecular Nanohelix Fabricated by Pillararene-Based Host–Guest System for Chirality Amplification, Transfer, and Circularly Polarized Luminescence in Water

Supramolecular Nanohelix Fabricated by Pillararene-Based Host–Guest System for Chirality Amplification, Transfer, and Circularly Polarized Luminescence in Water

Knoevenagel‐Cyclization Cascade Reactions of Substituted 5,6‐Dihydro‐2H‐Pyran Derivatives

AbstractThe diastereoselective domino‐Knoevenagel‐IMHDA reactions of 5,6‐dihydro‐2H‐pyran derivatives containing an o‐formylaryl amine or ether moiety were performed with active methylene reagents. In the spiro heterocyclic products representing a novel skeleton, a tetrahydroquinoline or chroman unit is fused with two pyran rings and the bridgehead carbon atoms are chirality centers formed diastereoselectively. Depending on the substitution pattern, a domino Knoevenagel‐[1,5]‐hydride shift‐cyclization sequence was identified as a competing pathway, which resulted in the formation of tetrahydroquinoline derivatives with a 5,6‐dihydro‐2H‐pyran‐3‐yl substituent. The relative configurations of the products were determined by means of the characteristic NOE correlations and single crystal X‐ray diffraction analysis. Antiproliferative activity assays of two products against A2780 and WM35 human cancer cell lines showed low micromolar IC50 values down to 2.99 μM.

Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon.

Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of CH correlations (-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The -HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon’s enhanced HMBC data processing capabilities. A systematic study of the CH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure.

Trikoveramides A-C, cyclic depsipeptides from the marine cyanobacterium Symploca hydnoides

Trikoveramides A – C, members of the kulolide superfamily of cyclic depsipeptides, were isolated from the marine cyanobacterium, Symploca hydnoides, collected from Bintan Island, Indonesia. Their planar structures were elucidated by a combination of NMR spectroscopy and HRMS spectral data. The absolute configurations of the amino acid and phenyllactic acid units were confirmed by Marfey's and chiral HPLC analyses, respectively, while the relative stereochemistry of the 3-hydroxy-2-methyl-7-octynoic acid (Hmoya) unit in trikoveramide A was elucidated by the application of the J-based configuration analysis and NOE correlations. The cytotoxic activity of the trikoveramides were evaluated against MOLT-4 human leukemia cells and gave IC50 values of 9.3 μM, 35.6 μM and 48.8 μM for trikoveramide B, trikoveramide C and trikoveramide A, respectively. In addition, trikoveramides A – C showed weak to moderate inhibition in the quorum sensing inhibitory assay based on the Pseudomonas aeruginosa lasB-gfp and rhlA-gfp bioreporter strains.

Magnetization Transfer to Enhance NOE Cross‐Peaks among Labile Protons: Applications to Imino–Imino Sequential Walks in SARS‐CoV‐2‐Derived RNAs

2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent‐driven exchanges to enhance NOE correlations between exchangeable and non‐exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino–imino cross‐peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS‐CoV‐2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.

Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs.

2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent‐driven exchanges to enhance NOE correlations between exchangeable and non‐exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino–imino cross‐peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS‐CoV‐2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.

Diterpenes from Euphorbia myrsinites and Their Anti-inflammatory Property.

Euphorbia myrsinites is one of the oldest spurges described and used in folk medicine. It is characterized by blue-grey stems similar to myrtle, and it is spread in the Mediterranean region, Asia, and the USA. Chemical analysis of E. myrsinites collected in Turkey afforded the isolation of 4 diterpenes based on the so-called myrsinane skeleton being tetraesters of the tetracyclic diterpene alcohol myrsinol. In this study, the phytochemical analysis of this species collected in Italy has been undertaken to afford the isolation of a new atisane diterpene, named myrsatisane, 3 ingenol derivatives, along with the 4 tetraester derivatives previously found. A triterpene compound based on the euphane skeleton has also been isolated. Structural elucidation of the new myrsatisane was based on spectroscopic techniques, including HR-MS and 1-and 2-dimensional NMR experiments. Its relative configuration was determined by NOE correlations, while absolute stereochemistry was obtained by quantum-mechanical DFT studies. While diterpenes with the atisane skeleton are relatively common in Euphorbia species, this is the first report of an atisane diterpene from E. myrsinites. All the isolated terpenes were tested for anti-inflammatory activity on J774A.1 macrophages stimulated with lipopolysaccharide by evaluation of nitrite and pro-inflammatory cytokine Il-1β levels. Among tested compounds, the 3 ingenol diterpenes exhibited a dose-dependent (0.001 - 3 µM) significant activity, thus showing their potential as anti-inflammatory drug candidates.