Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae.

BACKGROUND: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. RESULTS: The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. CONCLUSIONS: In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

Cascade Oxidative Trifluoromethylthiolation and Cyclization of 3-Alkyl-1-(2-(alkynyl)phenyl)indoles.

Persulfate-promoted radical cascade trifluoromethylthiolation and cyclization of 3-alkyl-1-(2-(alkynyl)phenyl)indoles with AgSCF3 were investigated. This protocol provides a novel route to CF3S-substituted indolo[1,2-a]quinoline-7-carbaldehydes and CF3S-substituted indolo[1,2-a]quinoline-7-methanone derivatives via the formation of the C-SCF3 bond and C-C bond and benzylic carbon oxidation in a single step. This reaction can accommodate a broad range of functional groups. The single-crystal X-ray diffraction data confirm the chemical structure of the product. A scale-up experiment and radical inhibition experiments were operated in the reaction system. Photophysical properties of some selected 5-((trifluoromethyl)thio)indolo[1,2-a]quinoline-7-carbaldehydes were studied by UV-visible and fluorescence spectroscopy.

Electrochemical trifluoromethylation of 2-isocyanobiaryls using CF3SO2Na: synthesis of 6-(trifluoromethyl)phenanthridines.

An efficient trifluoromethylation of 2-isocyanobiaryls was developed through the constant current electrolysis, employing sodium trifluoromethanesulfinate (CF3SO2Na) as the trifluoromethyl source. The method enabled the syntheses of a series of 6-(trifluoromethyl)phenanthridine derivatives in moderate to high yields under metal- and oxidant-free conditions. A gram-scale synthesis highlights the synthetic versatility of the reported protocol.

Base-catalyzed diastereodivergent thia-Michael addition to chiral ß-trifluoromethyl-α,ß-unsaturated N-acylated oxazolidin-2-ones.

Base-catalyzed diastereodivergent thia-Michael addition of thiols to chiral ß-trifluoromethyl-α,ß-unsaturated N-acylated oxazolidin-2-ones is reported. By tuning the base-catalyst (i-Pr2NEt, DABCO, or P2-t-Bu), a range of chiral thia-Michael adducts was synthesized in good yields with high diastereoselectivities. A plausible mechanism was proposed on the basis of the experimental results. This work is complementary to the existing methods offering advantages, e.g., switchable diastereoselectivity using a readily synthesized chiral starting material, a cheap and readily available base catalyst, and a simple and practical operation, enabling synthetic application in organic synthesis.

Pyranonaphthoquinones and Naphthoquinones from the Stem Bark of Ventilago harmandiana and Their Anti-HIV-1 Activity.

Seven previously undescribed compounds, including five pyranonaphthoquinones (ventilanones L-P) and two naphthoquinones (ventilanones Q and R), along with 15 known compounds were isolated from the stem bark of Ventilago harmandiana (Rhamnaceae). The structures were established by extensive analysis of their spectroscopic data. The absolute configuration of ventilanone L was established from single crystal X-ray crystallographic analysis using Cu Kα radiation and from its electronic circular dichroism data. Anti-HIV-1 activity using a syncytium inhibition assay and the cytotoxic activities of some isolated compounds were evaluated. Compounds 12, 13, 15, and 16 showed activity against syncytium formation with half maximal effective concentration (EC50) values ranging from 9.9 to 47 µM (selectivity index (SI) 2.4-4.5).

Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre.

The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight MS (UPLC-TWIMS-QTOF), we have established and validated a comprehensive TWCCSN2 and MS database for 112 plant specialized metabolites. The database included 15 compounds that were isolated and purified in-house and are not commercially available. We obtained accurate m/z, retention times, fragment ions, and TWIMS-derived CCS (TWCCSN2) values for 207 adducts (ESI+ and ESI-). The database included novel 158 TWCCSN2 values from 79 specialized metabolites. In the presence of plant matrix, the CCS measurement was reproducible and robust. Finally, we demonstrated the application of the database to extend the metabolite coverage of Ventilago harmandiana Pierre. In addition to pyranonaphthoquinones, a group of known specialized metabolites in V. harmandiana, we identified flavonoids, xanthone, naphthofuran, and protocatechuic acid for the first time through targeted analysis. Interestingly, further investigation using IM-MS of unknown features suggested the presence of organonitrogen compounds and lipid and lipid-like molecules, which is also reported for the first time. Data are available on the MassIVE (https://massive.ucsd.edu, data set identifier MSV000090213).

Diastereoselective Addition of PhSCF2SiMe3 to Chiral N-tert-Butanesulfinyl Ketimines Derived from Isatins: Synthesis of Enantioenriched gem-Difluoromethylenated Spiro-pyrrolidinyl and Spiro-piperidinyl Oxindoles.

A convenient and efficient synthetic strategy to prepare enantioenriched gem-difluoromethylenated spiro-pyrrolidinyl and spiro-piperidinyl oxindoles is described. Fluoride-mediated diastereoselective nucleophilic addition of PhSCF2SiMe3 to chiral N-tert-butanesulfinyl ketimines derived from isatins was a key step and provided diastereomeric adducts, which were readily separable. Removal of the chiral sulfinyl group followed by structural manipulation afforded chiral gem-difluoromethylenated spiro-pyrrolidinyl and spiro-piperidinyl oxindoles.

Mass spectral analysis of secondary metabolites from Zingiber montanum rhizome extract using UHPLC-HR-ESI-QTOF-MS/MS.

INTRODUCTION: Zingiber montanum (J.Koenig) Link ex A.Dietr. is a popular medicinal plant in Thailand. Its rhizomes have been used as an ingredient in various Thai traditional medicine formulas. While many reports have focused on the chemical constituents and biological activities of this plant, a comprehensive study on secondary metabolite profiling using tandem mass spectrometry has, to this point, never been documented. OBJECTIVE: To analyze the chemical constituents in Z. montanum rhizomes using ultra-high performance liquid chromatography coupled with ultra-high-resolution electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC-HR-ESI-QTOF-MS/MS) analyses and to utilize the characteristic fragmentation patterns of these compounds to facilitate their identification. METHODOLOGY: UHPLC-HR-ESI-QTOF-MS/MS in positive ion mode was used for chemical identification of secondary metabolites from the ethanolic extract of the plant material. MS/MS data of some known reference compounds, together with detailed fragmentation pattern information of several compounds obtained from the crude extract, were used to elucidate their chemical structures. RESULTS: In this work, one benzaldehyde, ten phenylbutenoid monomers, six curcuminoids, and nine phenylbutenoid dimers were assigned based on their characteristic fragment ions. Among these compounds, 2-(3,4-dimethoxystyryl)oxirane was tentatively suggested as a potential new compound. Several characteristic fragment ions from these compounds were assigned and the relative ion abundance of these was also used to differentiate the chemical structures of compounds having the same molecular mass. CONCLUSIONS: The results will benefit future high-throughput screening of bioactive compounds and method development for the quality control of raw materials and herbal drugs derived from Z. montanum rhizome extracts.

Anti-Inflammatory Effects of Mitrephora sirikitiae Leaf Extract and Isolated Lignans in RAW 264.7 Cells.

Mitrephora sirikitiae Weeras., Chalermglin & R.M.K. Saunders has been reported as a rich source of lignans that contribute to biological activities and health benefits. However, cellular anti-inflammatory effects of M. sirikitiae leaves and their lignan compounds have not been fully elucidated. Therefore, this study aimed to investigate the anti-inflammatory activities of methanol extract of M. sirikitiae leaves and their lignan constituents on lipopolysaccharide (LPS)-induced inflammation in RAW 264.7 mouse macrophage cells. Treatment of RAW 264.7 cells with the methanol extract of M. sirikitiae leaves and its isolated lignans, including (-)-phylligenin (2) and 3',4-O-dimethylcedrusin (6) significantly decreased LPS-induced prostaglandin E2 (PGE2) and nitric oxide (NO) productions. These inhibitory effects of the extract and isolated lignans on LPS-induced upregulation of PGE2 and NO productions were derived from the suppression of cyclooxygenase 2 (COX-2) and inducible nitric oxide synthase (iNOS) production, respectively. In addition, treatment with 2-(3,4-dimethoxyphenyl)-6-(3,5-dimethoxyphenyl)-3,7-dioxabicyclo[3.3.0]octane (3) and mitrephoran (5) was able to suppress LPS-induced tumor necrosis factor alpha (TNF-α) secretion and synthesis in RAW 264.7 cells. These results demonstrated that M. sirikitiae leaves and some isolated lignans exhibited potent anti-inflammatory activity through the inhibition of secretion and synthesis of PGE2, NO, and TNF-α.

Boesenmaxane Diterpenoids from Boesenbergia maxwellii.

Three new diterpenoids, boesenmaxanes A-C (1-3), with an unprecedented core skeleton consisting of an unusual C-C bond between C-12 and an exo-cyclic methylene C-13, were isolated from the rhizome extracts of Boesenbergia maxwellii. The structures were elucidated by analysis of spectroscopic and X-ray diffraction data. Electronic circular dichroism spectra were used to determine the absolute configuration. All the isolates were evaluated for their cytotoxic effects, anti-HIV activity, and antimicrobial activity. Boesenmaxanes A and C (1 and 3) showed significant inhibitory activity in the syncytium reduction assay, with EC50 values of 55.2 and 27.5 µM, respectively.

Alkanethiol-Mediated Cyclization of o-Alkynylisocyanobenzenes: Synthesis of Bis-Thiolated Indole Derivatives.

Reactions of o-alkynylisocyanobenzenes with a variety of alkanethiols (Alk-SH) provide the corresponding bis-thiolated indole derivatives. The advantages of the reaction include metal-free, room-temperature, mild reaction conditions and broad functional group compatibility. The reaction proceeds via nucleophilic addition of an alkanethiol to an isonitrile moiety, 5-exo cyclization, followed by nucleophilic addition of an alkanethiol to a 3-alkylidene indole intermediate. Density functional calculations on the electronic structures and relative free energies of 5-exo and 6-endo cyclization pathways support that the 5-exo cyclization is preferable.

Cytotoxic compounds from the leaves and stems of the endemic Thai plant Mitrephora sirikitiae.

Context: Mitrephora sirikitiae Weeras., Chalermglin & R.M.K. Saunders (Annonaceae) is a plant endemic to Thailand. Its constituents and their biological activities are unknown.Objective: Isolation and identification of the compounds in the leaves and stems of M. sirikitiae and determination of their cytotoxicity.Materials and methods: Methanol extracts of the leaves and stems of M. sirikitiae were separated by chromatography, and spectroscopic methods were used to determine the structures of the components. The cytotoxicity of the extracts and pure compounds was evaluated using the sulforhodamine B assay with several cell lines. The cells were treated with the compounds at concentrations of 0.16-20 µg/mL for 48 or 72 h.Results: The investigation of the extracts of M. sirikitiae leaves and stems resulted in the isolation of a new lignan, mitrephoran, and 15 known compounds. Among these compounds, 2-(3,4-dimethoxyphenyl)-6-(3,5-dimethoxyphenyl)-3,7-dioxabicyclo[3.3.0]octane, ciliaric acid, 6-methoxymarcanine A, and stepharanine were isolated from this genus for the first time. The alkaloids liriodenine and oxoputerine exhibited strong cytotoxicity against all tested cells (IC50 values of 6.59-11.02 µM). In contrast, magnone A, 3',4-O-dimethylcedrusin, and 6-methoxymarcanine A inhibited the growth of some of the tested cells (IC50 values of 2.03-19.73 µM). Magnone A and 6-methoxymarcanine A showed low toxicity for Hek 293 cells (IC50 >20 µM).Discussion and conclusions: M. sirikitiae is a source of cytotoxic lignans and alkaloids. Among the cytotoxic compounds, magnone A and 6-methoxymarcanine A are potentially useful lead compounds for the further development of anticancer agents because of their selective inhibitory effects on cancer cell lines.

Synthesis of Indolo- and Benzothieno[2,3-b]quinolines by a Cascade Cyclization of o-Alkynylisocyanobenzene Derivatives.

A new synthetic approach for the synthesis of indolo[2,3-b]quinolines and benzothieno[2,3-b]quinolines has been developed by employing the freshly prepared o-alkynylisocyanobenzenes derived from o-alkynylformamide derivatives as substrates. The synthetic transformations involved chloride-ion-triggered 6-endo cyclization of o-alkynylisocyanobenzenes to generate 2-chloroquinolines in situ, which further cyclized intramolecularly with nitrogen or sulfur atom via a cascade process to provide the corresponding indolo[2,3-b]quinolines and benzothieno[2,3-b]quinolines, respectively, in moderate to excellent yields.

Synthesis of C2-Symmetric gem-Difluoromethylenated Angular Triquinanes.

A synthesis of symmetrical gem-difluoromethylenated angular triquinanes is described. The synthetic strategy involved sequential fluoride-catalyzed nucleophilic addition of PhSCF2SiMe3 (1) to 2,2-diallylated or 2,2-dipropargylated indane-1,3-diones 2 followed by stereoselective radical cyclization of the resulting adducts 3 to provide the cyclized gem-difluoromethylenated diquinanes 4 as a mixture of stereoisomers. Repeated addition of 1 to 4 followed by cyclization resulted in the stereoselective synthesis of the desired C2-symmetric gem-difluoromethylenated angular triquinanes 6 in good yields with high stereoselectivity.

Oxidative Difluoromethylation of Tetrahydroisoquinolines Using TMSCF2SPh: Synthesis of Fluorinated Pyrrolo[2,1-a]isoquinolines and Benzo[a]quinolizidines.

An efficient C1-difluoromethylation of tetrahydroisoquinolenes was achieved using TMSCF2SPh as a difluoromethylating agent and 2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (TEMPO+BF4-) as an oxidant. The process provides an access to a variety of C1-difluoro(phenylsulfanyl)methylated tetrahydroisoquinoline adducts in good yields. These adducts were employed as key precursors for preparing fluorinated pyrrolo[2,1-a]isoquinoline and benzo[a]quinolizidines.

Bioinspired Asymmetric Synthesis of (-)-Gymnothelignan V.

A bioinspired asymmetric total synthesis of a structurally unique subtype of lignan, namely, (-)-gymnothelignan V, was achieved. The key synthetic sequences involved reduction of the eupomatilone skeleton leading to (-)-gymnothelignan J followed by the formation of the corresponding oxocarbenium ion and stereoselective intramolecular Friedel-Crafts reaction. Our synthetic approach provides the information to support the plausible biosynthetic pathway of this structurally unusual lignan. On a similar basis, other structurally related natural and non-natural gymnothelignans including (-)-gymnothelignan D, 6,9-bis- epi-gymnothelignan V, and 5- epi-gymnothelignans D and J were readily prepared.

Sulfinates and thiocyanates triggered 6-endo cyclization of o-alkynylisocyanobenzenes.

Diverse 2-sulfonyl- and 2-thiocyanato-3-substituted quinolines were synthesized from o-alkynylisocyanobenzenes by nucleophilic addition of the respective sulfinate sodium salts and ammonium thiocyanate to the isocyanide moiety followed by cyclization. The salient features of the methodology include metal-free, ambient temperature and mild reaction conditions, ease of reagent handling, and broad functional group tolerance.

Synthesis of 3-substituted quinolin-2(1H)-ones via the cyclization of o-alkynylisocyanobenzenes.

A facile synthesis of various functionalized 3-substituted quinolin-2(1H)-ones through Ag(i) nitrate-catalyzed cyclization of o-alkynylisocyanobenzenes is described. The reaction allows rapid and convenient access to 3-substituted quinolin-2(1H)-one scaffolds in moderate to good yields.

Asymmetric synthesis of ent-fragransin C1.

The first asymmetric synthesis of ent-fragransin C1 was reported. The key step involves an intramolecular C-O bond formation (furan ring formation) via chemoselective generation of the benzylic carbocation leading to the 2,3-anti-3,4-syn-4,5-anti-tetrahydrofuran moiety as a single diastereomer in good yield. Our synthesis confirms that ent-fragransin C1 possesses 2R,3R,4S,5S configurations.

Synthesis of N-alkyl-3-sulfonylindoles and N-alkyl-3-sulfanylindoles by cascade annulation of 2-alkynyl-N,N-dialkylanilines.

An efficient and metal-free approach to N-alkyl-3-sulfonylindoles and N-alkyl-3-sulfanylindoles from 2-alkynyl-N,N-dialkylanilines has been developed. In the presence of iodine and tert-butylhydroperoxide (TBHP), a variety of 2-alkynyl-N,N-dialkylanilines underwent a cascade radical annulation to yield 3-arylsulfonylindoles. In contrast, 3-arylsulfanylindoles were conveniently prepared by iodine mediated electrophilic annulation reactions. The present protocol uses the economical and environmentally friendly I2-TBHP or I2 system, and potentially bioactive N-alkyl-3-sulfonylindoles and N-alkyl-3-sulfanylindoles with various functional groups were successfully synthesized in moderate to good yields.