NMR spectroscopic method for the assignment of 3,5-dioxygenated aromatic rings in natural products

Clinical development and informatics analysis of natural and semi-synthetic flavonoid drugs: A critical review

BACKGROUND

Flavonoids are one of the most important metabolites with vast structural diversity and a plethora of potential pharmacological applications, which have drawn considerable attention in the laboratory. Nevertheless, it remains uncertain how many candidates were progressed to clinical application.

AIM OF REVIEW

We carried out a critical review of natural and semi-synthetic flavonoid drugs and candidates undergoing different clinical phases worldwide by applying an adequate search method and conducted a brief cheminformatic and bioinformatic analysis. It was expected that the obtained results might narrow the screening scope and reduce the cost of drug research and development.

KEY SCIENTIFIC CONCEPTS OF REVIEW

To our knowledge, this is the most systematic summarization of flavonoid-based drugs and clinical candidates to date. It was found that a total of 19 flavonoid-based drugs have been approved for the market, and of these, natural flavonoids accounted for 52.6%. Besides, a total of 36 flavonoid-based clinical candidates are undergoing or suspended in different phases, and of these, natural flavonoids account for 44.4%. Thus, natural flavonoids remain the best option for finding novel agents/active templates, and when investigated in conjunction with synthetic chemicals and biologicals, they offer the potential to discover novel structures that can lead to effective agents against a variety of human diseases. Additionally, flavonoid-based marketed drugs have been successful in cardiovascular treatment, and the related drugs account for more than 30% of marketed drugs. However, the use of flavonoids as antineoplastic and immunomodulating agents is not likely for approximately 50% of the candidates suspended in the clinical stage. Interestingly, the marketed drugs covered a broader range of chemical spaces based on size, polarity, and three-dimensional structure compared to the clinical candidates. In addition, flavonoid glycosides with poor oral bioavailability account for 36.8% of the marketed drugs, and thus, they could be thoroughly investigated.

Rapid determination of the relative configuration of diverse 8,4'-oxyneolignans by NMR analysis: Retrospective studies, improvement and structural revision

The characteristic 1H NMR signals (H-7 and H2-9) are significant parameters that have been widely used to assess the relative configuration of H-7 and H-8 of 8,4'-oxyneolignans. However, many usual 8,4'-oxyneolignans cannot be accurately determined by existing NMR methods and no research considering their limitations was performed until now. In this study, the application scope of NMR methods was comprehensively studied and the ΔδH9a-H9b methods have been extended to solve the majority of configuration determination difficulties. The accuracy of extended NMR methods was verified by anisotropic NMR (RCSA measurements), NMR calculation and diverse statistical analysis (MAEΔΔδ, CP3 and DP4+). Furthermore, the theoretical conformational analysis was performed to investigate the inherent limitations of existing NMR methods. This study could provide a valuable reference for determining the relative configuration of H-7 and H-8 in 8,4'-oxyneolignans and the relative configuration of 23 recently reported 8,4'-oxyneolignan derivatives should be reassigned as well.

Sumatranins A-J: Lignans with Immunosuppressive Activity from Cleistanthus sumatranus

Chemical investigation of the twigs of Cleistanthus sumatranus (Phyllanthaceae) led to the isolation of 10 undescribed lignans, sumatranins A-J (1-10). Compounds 1-4 are unprecedented furopyran lignans characterized by a unique 2,3,3a,9a-tetrahydro-4H-furo[2,3-b]chromene heterotricyclic framework. Compounds 9 and 10 are rare 9'-nor-dibenzylbutane lignans. Structures were established based on analyses of spectroscopic data, X-ray crystallographic data, and experimental ECD spectra. Immunosuppressive assays revealed compounds 3 and 9 displayed moderate inhibitory effects with good selectivity indexes against LPS-induced B lymphocyte proliferation.

Aromatic diglycosides from Sophora tonkinensis and a multi-step conformer filtering procedure for TDDFT calculation of flexible glycoside

Three previously undescribed aromatic diglycosides (1, 5, and 8) and six known analogs (2-4, 6, 7, and 9) were isolated from the roots and rhizomes of Sophora tonkinensis Gagnep. Their structures were elucidated by detailed spectroscopic analysis. The absolute configuration of compound 8 was determined by comparing the experimental and TDDFT calculated ECD spectra of 8 and aglycone 8a. Furthermore, a multistep conformer filtering procedure for TDDFT calculation of flexible glycoside was proposed, which afforded high accuracy with acceptable computing cost in determining the absolute configuration of glycosides using quantum calculated ECD.

Conditional Molecular Generation Net Enables Automated Structure Elucidation Based on 13C NMR Spectra and Prior Knowledge

Structure elucidation of unknown compounds based on nuclear magnetic resonance (NMR) remains a challenging problem in both synthetic organic and natural product chemistry. Library matching has been an efficient method to assist structure elucidation. However, it is limited by the coverage of libraries. In addition, prior knowledge such as molecular fragments is neglected. To solve the problem, we propose a conditional molecular generation net (CMGNet) to allow input of multiple sources of information. CMGNet not only uses ¹³C NMR spectrum data as input but molecular formulas and fragments of molecules are also employed as input conditions. Our model applies large-scale pretraining for molecular understanding and fine-tuning on two NMR spectral data sets of different granularity levels to accommodate structure elucidation tasks. CMGNet generates structures based on ¹³C NMR data, molecular formula, and fragment information, with a recovery rate of 94.17% in the top 10 recommendations. In addition, the generative model performed well in the generation of various classes of compounds and in the structural revision task. CMGNet has a deep understanding of molecular connectivities from ¹³C NMR, molecular formula, and fragments, paving the way for a new paradigm of deep learning-assisted inverse problem-solving.

Phenylpropanoids from Brachybotrys paridiformis maxim. Ex oliv. And their anti-HBV activities (II)

Five undescribed phenylpropanoids, one undescribed phenolic glucoside, and sixteen known compounds were isolated from Brachybotrys paridiformis Maxim. Ex Oliv. The undescribed compounds were named brachoside B-C, brach acid A-B, brachnan A, and brachin D, respectively. Additionally, the anti-hepatitis B virus activities of all isolated compounds were studied. Among them, brachnan A, brach acid A, globoidnan A, 3-carboxy-6,7-dihydroxy-1-(3',4'-dihydroxy-phenyl)-naphthalene, and 3,4-dihydroxybenzaldehyde showed significant anti-hepatitis B virus activities.

Highly Oxidized Germacranolides from Elephantopus tomentosus and the Configurational Revision of Some Previously Reported Analogues

Highly oxidized germacranolides are mainly found in the genus Elephantopus, contain a characteristic ten-membered molecular core that is highly flexible, and exhibit potential cytotoxic properties. However, their configurations were assigned ambiguously in previous reports due to spectroscopic observation of macrocyclic systems. Herein, 17 highly oxidized germacranolides, including 12 new germacranolides (1-12), were isolated from Elephantopus tomentosus. Their structures were characterized by spectroscopic data analysis combined with X-ray crystallography and ECD calculations, and it was possible to propose configurational revisions of five previously reported analogues (13-17). Cytotoxic activities for 1-17 against two hepatocellular carcinoma cell lines (HepG2 and Hep3B) were tested, and compounds 1-10 and 13-16 generated IC₅₀ values of 2.2-9.8 μM. Furthermore, the observed cytotoxic activity of 1 was determined as being mediated by inducing the apoptosis of HepG2 and Hep3B cells via mitochondrial dysfunction.

Unusual polyoxygenated casbane diterpenoids from the South China Sea soft coral Sinularia erecta

A further systematically chemical investigation of the South China Sea soft coral Sinularia erecta led to the discovery of two rare casbane diterpenoids with an uncommon 8,10-peroxide bridge, sinuereperoxides B (1) and C (2), five new casbanes with other oxygenated patterns (3-7), and seven known casbanes (8-14). The structures and absolute configurations of 1-7 were established by extensive spectroscopic data analyses, X-ray diffraction analysis, and/or quantum chemical calculations. In bioassay, compounds 2, 7, 11 and 12 exhibited considerable anti-inflammatory activity by the inhibition of TNF-α release, with IC₅₀ values of 33.8 μM, 5 μM, 9.9 μM and 8 μM.

Furofuranone Lignans from Leucophyllum ambiguum

Eight furofuranone lignans with an endo,endo relationship between the oxygen atoms, an exo,exo relationship between the aryl groups, and a chair,chair conformation (1-4 and 6-9), in addition to the α-amino acid (3S)-hydroxy-3',4'-dimethoxy-L-phenylalanine (5), veratric acid (10), and β-sitosterol (11), were isolated from the powdered and defatted air-dried aerial parts of Leucophyllum ambiguum. Four of these lignans, ciquitins A-D, 1-4, were isolated for the first time as natural products. The structures of these compounds were established based on their spectrometric/spectroscopic data. Additionally, single-crystal X-ray crystallography confirmed the structure of ciquitin A (1), and derivatization with (9S)-naproxen and X-ray diffraction crystallography data established its absolute configuration. Ciquitins A (1) and B (2) possess a 9-hydroxy group; this chemical characteristic grants these species conformational isomerism not seen in the other six lignans. The conformers of 1 and 2 are distinguishable via their ¹H and ¹³C NMR spectroscopic data. This is the first report of this phenomenon, and hence, a complete assignment of the signals in both spectra of each conformer for each compound is presented. Compounds 1-9 were found to exhibit potent inhibitory activity in the 1.0 × 10^-3 to 2.2 μM range against acetylcholinesterase, an enzyme directly involved in the etiology of Alzheimer's disease and senile dementia. Thus, these natural products are promising agents that are potentially useful for the treatment of neurological degeneration.

Seven new flavonoid glycosides from the roots of Glycyrrhiza uralensis and their biological activities

As part of our ongoing investigation of the bioactive constituents from the roots of Glycyrrhiza uralensis Fisch., seven new flavonoid glycosides (1-7) were obtained along with 19 known compounds (8-26). All of the isolates possessed one or more sugar moieties. Their structures, as well as the absolute configurations, were elucidated on the basis of spectroscopic data (UV, IR, HRESIMS, 1D and 2D NMR, and CD). In the in vitro assay, compounds 3 and 7 showed moderate antioxidant activities at a concentration of 0.1 μM; compound 2 showed hepatoprotective activity at a concentration of 10 μM.

Two pairs of phenylpropanoid enantiomers from the leaves of Eucommia ulmoides

Two pairs of phenylpropanoid enantiomers, (+)-(7S,8S)-alatusol D (1a), (-)-(7R,8R)-alatusol D (1b), (-)-(7S,8R)-alatusol D (2a) and (+)-(7R,8S)-alatusol D (2b) were isolated from the leaves of Eucommia ulmoides Oliver. Among them, 1a and 2b were firstly obtained by chiral enantiomeric resolution. Their structures were elucidated based on extensive spectroscopic analysis and the induced CD (ICD) spectrum caused by adding Mo₂(AcO)₄ in DMSO. All compounds were tested on Hep G2 tumor cell lines. However, none of the compounds showed potential cytotoxic activity against Hep G2 in vitro.

The Anticancer Activities Phenolic Amides from the Stem of Lycium barbarum

Four new phenolic amides, 4-O-methylgrossamide (1), (E)-2-(4,5-dihydroxy-2-{3-[(4-hydroxyphenethyl)amino]-3-oxopropyl}-phenyl)-3-(4-hydroxy-3-methoxyphenyl)-N-(4-hydroxyphenethyl)acryl-amide (2), (Z)-lyciumamide C (3), (Z)-thoreliamide B (4), together with thirteen known phenolic amides were identified from the stem of Lycium barbarum. The structures of the new compounds were determined by spectroscopic methods. All compounds were evaluated for their anti-cancer activities against human glioma stem cell lines.

Antarctic Moss Biflavonoids Show High Antioxidant and Ultraviolet-Screening Activity

Ceratodon purpureus is a cosmopolitan moss that survives some of the harshest places on Earth: from frozen Antarctica to hot South Australian deserts. In a study on the survival mechanisms of the species, nine compounds were isolated from Australian and Antarctic C. purpureus. This included five biflavonoids, with complete structural elucidation of 1 and 2 reported here for the first time, as well as an additional four known phenolic compounds. Dispersion-corrected DFT calculations suggested a rotational barrier, leading to atropisomerism, resulting in the presence of diastereomers for compound 2. All isolates absorbed strongly in the ultraviolet (UV) spectrum, e.g., biflavone 1 (UV-A, 315-400 nm), which displayed the strongest radical-scavenging activity, 13% more efficient than the standard rutin; p-coumaric acid and trans-ferulic acid showed the highest UV-B (280-315 nm) absorption. The more complex and abundant 1 and 2 presumably have dual roles as both UV-screening and antioxidant compounds. They are strongly bound to Antarctic moss cell walls as well as located inside the cells of moss from both locations. The combined high stability and photoprotective abilities of these isolates may account for the known resilience of this species to UV-B radiation and its survival in some of the toughest locations in the world.

Identification of a novel chalcone derivative that inhibits Notch signaling in T-cell acute lymphoblastic leukemia

Notch signaling is considered a rational target in the therapy of several cancers, particularly those harbouring Notch gain of function mutations, including T-cell acute lymphoblastic leukemia (T-ALL). Although currently available Notch-blocking agents are showing anti-tumor activity in preclinical studies, they are not effective in all the patients and often cause severe side-effects, limiting their widespread therapeutic use. Here, by functional and biological analysis of the most representative molecules of an in house library of natural products, we have designed and synthetized the chalcone-derivative 8 possessing Notch inhibitory activity at low micro molar concentration in T-ALL cell lines. Structure-activity relationships were afforded for the chalcone scaffold. Short term treatments with compound 8 resulted in a dose-dependent decrease of Notch signaling activity, halted cell cycle progression and induced apoptosis, thus affecting leukemia cell growth. Taken together, our data indicate that 8 is a novel Notch inhibitor, candidate for further investigation and development as an additional therapeutic option against Notch-dependent cancers.

Diterpenoids and Lignans from Cephalotaxus fortunei

Five new diterpenoids including two Cephalotaxus troponoids (1 and 2), two 17-nor-cephalotane-type diterpenoids (3 and 4), and an abietane-type diterpenoid (5), two new lignans (6 and 7), and a new trisnorneoligan (8) along with eight known compounds were identified from the twigs and leaves of Cephalotaxus fortunei. The structure of 11-hydroxyhainanolidol was revised as 10-hydroxyhainanolidol (9) by X-ray crystallographic data. Compounds 3 and 4 are the first examples of 17-nor-cephalotane-type diterpenoids that are likely the biosynthesis precursors of the co-occurring troponoids (e.g., 1, 2, and 9). Compound 1 exhibited cytotoxic activities against HL-60 and A-549 cells with IC₅₀ values of 0.77 ± 0.05 and 1.129 ± 0.057 μM, respectively.

Ailanthusins A-G and nor-lupane triterpenoids from Ailanthus triphysa

Bioactivity-guided chemical investigation of the CH₂Cl₂ and CH₂Cl₂MeOH extracts of the stem and stem bark material of Ailanthus tryphysa (Simaroubaceae) led to the isolation of five cycloapotirucallanes, ailanthusins A-E, two malabaricanes, ailanthusins F-G, and one nor-lupane triterpenoid, 29-nor-lup-1-ene-3,20-dione along with twenty known compounds. Their structures were elucidated through the application of extensive spectroscopic methods, and the structure of ailanthusin A was further confirmed by single crystal X-ray analysis. Several malabaricane derivatives were prepared from malabaricol and, together with some of the isolates, were evaluated for their cytotoxic activities against human cancer and normal cell lines.