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.

Antibacterial activity evaluation of vinyl sulfones against global predominant methicillin-resistant Staphylococcus aureus USA300.

The electrophilic potential of vinyl sulfone permits the rapid capture of cysteine-containing proteins under physiological conditions. These cysteine proteinases play vital roles in bacterial survival and pathogenesis of Staphylococcus aureus (S. aureus) and the global health threat methicillin resistant S. aureus (MRSA). Here in, total of 28 vinyl sulfones were synthesized and subjected to susceptibility testing of pathogenic bacteria, including global epidemic MRSA PFGE strain type USA300 (SF8300). Number of antibacterial vinyl sulfone derivatives were discovered. Among these, nitrile-substituted vinyl phenyl sulfones showed potent antibacterial activity. (E)-3-((4-methoxyphenyl)sulfonyl)acrylonitrile exhibited the strongest potency with MIC of 1.875 µg/mL against methicillin susceptible S. aureus and 3.75 µg/mL against MRSA USA300. Based on the structure-activity relationship analysis, the antibacterial activity of these compounds may involve sulfhydryl conjugation. In addition, the nitrile-substituted vinyl phenyl sulfone could also impair host cell adhesion. With their promising antibacterial activities, these vinyl sulfones have potential for S. aureus and MRSA therapeutics.

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.

Identification of Vinyl Sulfone Derivatives as EGFR Tyrosine Kinase Inhibitor: In Vitro and In Silico Studies.

Epidermal growth factor receptor (EGFR), overexpressed in many types of cancer, has been proved as a high potential target for targeted cancer therapy due to its role in regulating proliferation and survival of cancer cells. In the present study, a series of designed vinyl sulfone derivatives was screened against EGFR tyrosine kinase (EGFR-TK) using in silico and in vitro studies. The molecular docking results suggested that, among 78 vinyl sulfones, there were eight compounds that could interact well with the EGFR-TK at the ATP-binding site. Afterwards, these screened compounds were tested for the inhibitory activity towards EGFR-TK using ADP-Glo™ kinase assay, and we found that only VF16 compound exhibited promising inhibitory activity against EGFR-TK with the IC50 value of 7.85 ± 0.88 nM. In addition, VF16 showed a high cytotoxicity with IC50 values of 33.52 ± 2.57, 54.63 ± 0.09, and 30.38 ± 1.37 µM against the A431, A549, and H1975 cancer cell lines, respectively. From 500-ns MD simulation, the structural stability of VF16 in complex with EGFR-TK was quite stable, suggesting that this compound could be a novel small molecule inhibitor targeting EGFR-TK.

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.

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.

Iodine-catalyzed Sulfonylation of Arylacetylenic Acids and Arylacetylenes with Sodium Sulfinates: Synthesis of Arylacetylenic Sulfones.

A highly efficient and generally applicable iodine-catalyzed reaction of arylacetylenic acids and arylacetylenes with sodium sulfinates for the synthesis of arylacetylenic sulfones was developed. The methodology has the advantages of a metal-free strategy, easy to handle reagents, functional group tolerance, a wide range of arylacetylenic acids and arylacetylenes, and easy access to arylacetylenic sulfones.