Pegaharmols A–B, Axially Chiral β-Carboline-quinazoline Dimers from the Roots of Peganum harmala

Discovery of polycyclic polyprenylated acylphloroglucinols with antitumor activities from Garcinia pedunculata Roxb. fruits based on molecular networking

Garpedvinin A (1), a novel polycyclic polyprenylated acylphloroglucinol (PPAP) with a bicyclo[4,2,1]nonane core, 13 previously undescribed PPAPs, garpedvinins B-N (2-14) and 6 known analogs (15-20) were isolated from Garcinia pedunculata by various chromatographic methods combined with Global Natural Products Social Molecular Networking. The structures were identified by the analyses of spectral characteristics, computational chemistry calculations and single-crystal X-ray diffraction. A plausible biosynthetic pathway for garpedvinin A was suggested based on the isolated precursor, cambogin. Compounds 2-6, 8, 11, 13, 15-18 and 20 displayed cytotoxic effects on three cancer cell lines, HepG2, A549 and MCF-7. 6 showed the strong inhibitory effect on the proliferation of HepG2 cells in vitro, inducing cell apoptosis in a concentration-dependent manner and blocking the cell cycle at the S phase. Furthermore, 6 affected the expression of apoptosis-related proteins Bax, Bcl2 and pro-Caspase-3.

Catalytic Enantioconvergent Alkylation Reactions That Construct Chiral Quaternary Carbon Centers and Tune C(sp3)-C(sp2) Bond Rotation

In molecules with central chiral centers functionalized with aryl groups, the rotation of the single bond between the aryl group and the central chiral center may be hindered. Enantioconvergent alkylation reactions of racemic diastereomers to construct all-carbon quaternary stereocenters resulting in easing of the rotation around the axes are described. We demonstrated that the rotation of the bond between a central chiral carbon center and a dihydrobenzofuranone can be tuned by selection of either a tertiary carbon bearing a hydrogen or a quaternary carbon at the central chiral center. The products have the benefits of a central chiral center and a flexibly rotatable bond, which can facilitate interactions with other molecules.

Kopsileuconines A-D: Bisindole alkaloids with cytotoxic activity from Kopsia hainanensis

Kopsileuconines A-D (1-4), four monoterpenoid bisindole alkaloids with unprecedented skeletons, along with their biosynthetically related precursors (5-8) were isolated from the roots of Kopsia hainanensis. Compound 1 possessed an undescribed C-6-C-5' dimerization pattern of aspidofractinine-type alkaloids. Compounds 2-4 were rhazinilam-kopsine (2) and rhazinilam-aspidofractinine type (3 and 4) bisindole alkaloids with undescribed skeletons, respectively. Their structures with absolute configurations were fully accomplished by extensive spectroscopic analysis, quantum-chemical calculations, and X-ray crystallography. A plausible biosynthetic pathway for 1-4 was proposed. Compound 2 exhibited a significant inhibitory effect against human lung cancer cell lines PC9 (EGFR mutant), with an IC50 value of 15.07 ± 1.19 μM.

Enantioselective synthesis of molecules with multiple stereogenic elements

This review explores the fascinating world of molecules featuring multiple stereogenic elements, unraveling the different strategies designed over the years for their enantioselective synthesis. Specifically, (dynamic) kinetic resolutions, desymmetrisations and simultaneous installation of stereogenic elements exploiting either metal- or organo-catalysis are the principal approaches to efficiently create and control the three-dimensional shapes of these attractive molecules. Although most molecules presented in this review possess a stereogenic carbon atom in combination with a stereogenic axis, other combinations with helices or planes of chirality have started to emerge, as well as molecules displaying more than two different stereogenic elements.

Conformation Analysis and Stereodynamics of Symmetrically ortho-Disubstituted Carvacrol Derivatives

The design and synthesis of analogs of natural products can be a valuable source of medicinal preparations for the pharmaceutical industry. In the present study, the structural elucidation of eleven derivatives of 2,4-dihalogeno substituted synthetic analogues of the natural compound carvacrol was carried out by means of NMR experiments, and of another thirteen by DFT calculations. By selective NOE experiments and the irradiation of CH signals of the isopropyl group, individual conformers were assigned as syn and anti. By comparing GIAO/B3LYP/6-311++G(d,p)-calculated and experimentally measured vicinal 3JCH spin-spin constants, this assignment was confirmed. An unusual relationship is reported for proton-carbon vicinal couplings: 3JCH (180°) < 3JCH (0°). The conformational mobility of carvacrols was studied by 2D EXSY spectra. The application of homonuclear decoupling technique (HOBS) to these spectra simplifies the spectra, improves resolution without reducing the sensitivity, and allows a systematic examination of the rotational barrier of all compounds via their CH signals of the isopropyl group in a wider temperature interval. The rate constants of the isopropyl rotation between syn and anti conformers were determined and the corresponding energy barriers (14-17 kcal/mol) were calculated. DFT calculations of the energy barriers in carvacrol derivatives allowed the determination of the steric origin of the restricted isopropyl rotation. The barrier height depends on the size of the 2- and 4-position substituents, and is independent of the derivatization of the OH group.

Bioassay-guided isolation of anti-leukemic steroids from Aglaia abbreviata by inducing apoptosis

The strategy of bioactivity-guided isolation is widely used to obtain active compounds as quickly as possible. Thus, the inhibitory effects on human erythroleukemia cells (HEL) were applied to guide the isolation of the anti-leukemic compounds from Aglaia abbreviata. As a result, 19 compounds (16 steroids, two phenol derivatives, and a rare C12 chain nor-sesquiterpenoid), including 13 new compounds, were isolated and identified based on spectroscopic data analysis, single-crystal X-ray diffraction data, and electronic circular dichroism (ECD) calculations. Among them, 9 steroids exhibited good selective anti-leukemic activity against HEL and K562 (human chronic myeloid leukemia cells) cells with IC50 values between 2.29 ± 0.18 μM and 19.58 ± 0.13 μM. Notably, all the active compounds had relatively lower toxicity on the normal human liver cell line (HL-7702). Furthermore, five compounds (1, 4, 8, 10, and 19) displayed good anti-inflammatory effects, with IC50 values between 7.15 ± 0.16 and 27.1 ± 0.37 μM. An α,β-unsaturated ketone or a 5,6Δ double bond was crucial for improving anti-leukemic effect from the structure-activity relationship analysis. The compound with the most potential, 14 was selected for the preliminary mechanistic study. Compound 14 can induce apoptosis and cause cell cycle arrest. The expression of the marker proteins, such as PARP and caspase 3, were notably effected by this compound, thus inducing apoptosis. In conclusion, our investigation implied that compound 14 may serve as a potential anti-leukemia agent.

β-Carboline alkaloids from the roots of Peganum harmala L

This study reports the isolation of four new β-carboline alkaloids (1-4) and six previously identified alkaloids (5-10) from the roots of Peganum harmala L. Among these compounds, 1 and 2 were characterized as rare β-carboline-quinazoline dimers exhibiting axial chirality. Compound 3 possessed a unique 6/5/6/7 tetracyclic ring system with an azepine ring, and compound 4 was a novel annomontine β-carboline. The structures of these compounds were elucidated by spectroscopic data and quantum mechanical calculations. The biosynthetic pathways of 1-3 were proposed. Additionally, the cytotoxicity of some isolates against four cancer cell lines (HL-60, A549, MDA-MB-231, and DU145) was evaluated. Notably, compound 4 exhibited significant cytotoxicity against HL-60, A549, and DU145 cells with IC50 values of 12.39, 12.80, and 30.65 μmol·L-1, respectively. Furthermore, compound 2 demonstrated selective cytotoxicity against HL-60 cells with an IC50 value of 17.32 μmol·L-1.

Ring-fused hexahydro-1,2,4,5-tetrazines: synthesis, structure, and mechanistic studies on isolable rotational isomers

We designed conformationally stable rotational isomers around the C(sp²)-C(sp³) axis at the C₃-position of hexahydro-1,2,4,5-tetrazines. Isolation of each rotamer by silica gel column chromatography was successfully achieved at room temperature. The proposed isomerization mechanism of the rotamers was supported by NMR kinetic studies.

Hypersampones A-C, Three Nor-Polycyclic Polyprenylated Acylphloroglucinols with Lipid-Lowering Activity from Hypericum sampsonii

Hypersampones A-C (1-3), three unprecedented nor-polycyclic polyprenylated acylphloroglucinols (PPAPs), were isolated from Hypericum sampsonii. These compounds represent the first nor-PPAPs with an unexpected tetracyclic 6/5/5/6 ring system. Their structures were assigned through the analysis of detailed spectroscopic data, X-ray crystallography, and electronic circular dichroism calculations. Compound 1 significantly inhibited the accumulation of lipid in an oleic acid-treated HepG2 cell model by suppressing the protein expression of FAS and ACACA at 5 μM.

Anti-tumor alkaloids from Peganum harmala

Six alkaloids peharmalines F-K, along with 14 known ones, were isolated from the aerial part of Peganum harmala L.. The structures of the isolated compounds were determined based on their HR-ESI-MS data, extensive NMR spectroscopic analyses, and ECD calculations. 3-(4-Hydroxyphenyl)quinoline exhibited potent antiproliferative activity against the HepG-2 cell lines with an IC₅₀ value of 3.05 μM. Norharmane displayed a moderate inhibition against A549 and HepG-2 cells with IC₅₀ values of 16.45 μM and 17.27 μM, respectively.

Synthesis of pyrimidine-containing alkaloids

This review deals with the synthesis of naturally occurring alkaloids containing partially or completely saturated pyrimidine nuclei. The interest in these compounds is associated with their structural diversity, high biological activity and toxicity. The review is divided into four parts, each of which describes a number of synthetic methodologies toward structurally different naturally occurring alkaloids containing saturated cyclic six-membered amidine, guanidine, aminal and urea (thiourea) moieties, respectively. The development of various synthetic strategies for the preparation of these compounds has remarkably increased during the past few decades. This is primarily due to the fact that some of these compounds are isolated only in limited quantities, which makes it practically impossible to study their full structural characteristics and biological activity.

Organocatalytic Enantioselective Construction of Conformationally Stable C(sp2)-C(sp3) Atropisomers

Nonbiaryl atropisomers are molecules defined by a stereogenic axis featuring at least one nonarene moiety. Among these, scaffolds bearing a conformationally stable C(sp²)-C(sp³) stereogenic axis have been observed in natural compounds; however, their enantioselective synthesis remains almost completely unexplored. Herein we disclose a new class of chiral C(sp²)-C(sp³) atropisomers obtained with high levels of stereoselectivity (up to 99% ee) by means of an organocatalytic asymmetric methodology. Multiple molecular motifs could be embedded in this class of C(sp²)-C(sp³) atropisomers, showing a broad and general protocol. Experimental data provide strong evidence of the conformational stability of the C(sp²)-C(sp³) stereogenic axis (up to t_1/2^25 °C >1000 y) in the obtained compounds and show kinetic control over this rare stereogenic element. This, coupled with density functional theory calculations, suggests that the observed stereoselectivity arises from a Curtin-Hammett scenario establishing an equilibrium of intermediates. Furthermore, the experimental investigation led to evidence of the operating principle of central-to-axial chirality conversions.

Biology of quinoline and quinazoline alkaloids

Quinoline and quinazoline alkaloids, two important classes of N-based heterocyclic compounds, have attracted scientific and popular interest worldwide since the 19th century. More than 600 compounds have been isolated from nature to date. To build on our two prior reviews, we reexamined the promising molecules described in previous reports and provided updated literature on novel quinoline and quinazoline alkaloids isolated over the past 5 years. This chapter reviews and discusses 205 molecules with a broad range of bioactivities, including antiparasitic and insecticidal, antibacterial and antifungal, cardioprotective, antiviral, anti-inflammatory, and other effects. This survey should provide new clues or possibilities for the discovery of new and better drugs from the original naturally occurring quinoline and quinazoline alkaloids.

(±)-Pheharmines A–B, two pairs of racemic alkaloids with a morpholino[4,3,2-hi]β-carboline core, from the roots of Peganum harmala

Two pairs of unprecedented β-carboline-phenylpropanoid alkaloids, (±)-pheharmines A–B (1–4), characterized by a morpholino[4,3,2-hi]β-carboline core with two chiral centers, were isolated from the roots of Peganum harmala.

Survey of natural products reported by Asian research groups in 2020

The new natural products reported in 2020 in peer-reviewed articles in journals with good reputations were reviewed and analyzed. The advances made by Asian research groups in the field of natural products chemistry in 2020 were summarized. Compounds with unique structural features and/or promising bioactivities originating from Asian natural sources were discussed based on their structural classification.

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning

Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin ( https://tm.gdb.tools/map4/coconut_tmap/ ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance ( https://np-svm-map4.gdb.tools/ ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.

A comprehensive overview of β-carbolines and its derivatives as anticancer agents

β-Carboline alkaloids are a family of natural and synthetic products with structural diversity and outstanding antitumor activities. This review summarizes research developments of β-carboline and its derivatives as anticancer agents, which focused on both natural and synthetic monomers as well as dimers. In addition, the structure-activity relationship (SAR) analysis of β-carboline monomers and dimers are summarized and mechanism of action of β-carboline and its derivatives are also presented. A few possible research directions, suggestions and clues for future work on the development of novel β-carboline-based anticancer agents with improved expected activities and lesser toxicity are also provided.

A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide

Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.