All Natural: The Renaissance of Natural Products Chemistry

Cu(II) Promoted C(sp3 )-H Activation in Unactivated Cycloalkanes: Oxo-Alkylation of Styrenes to Synthesize β-Disubstituted Ketones

We report the Cu(II) catalyzed synthesis of β-disubstituted ketones from styrene via oxo-alkylation with unactivated cycloalkanes as the alkylating agent in presence of tert-butylhydroperoxide (TBHP) and 1-methylimidazole as oxidant and base respectively. β-disubstituted ketones are known to be synthesized by using either expensive Ru/Ir complexes, or low-cost metal complexes (e. g., Fe, Mn) with activated species like aldehyde, acid, alcohol, or phthalimide derivatives as the alkylating agent, however, use of unactivated cycloalkanes directly as the alkylating agent remains challenging. A wide range of aliphatic C-H substrates as well as various olefinic arenes and heteroarene (35 substrates including 14 new substrates) are well-tolerated in this method. Hammett analysis shed more light on the substitution effect in the olefinic part on the overall mechanism. Furthermore, the controlled experiments, kinetic isotope effect study, and theoretical calculations (DFT) enable us to gain deeper insight of mechanistic intricacies of this new simple and atom-economic methodology.

Dimeric N-Acetyldopamine Derivatives Featuring a Seco-Benzene System from the Insects Aspongopus chinensis and Periostracum cicadae

Aspongamide F (1), a novel N-acetyldopamine (NADA) dimer possessing a 6/6/6 ring system, and (±)-aspongamides G (2) and H (3), rare NADA derivatives with fragmented benzene rings, were isolated from Aspongopus chinensis. (±)-Cicadamides C (4) and D (5), the first 1,4-Benzodioxane NADA dimers featuring a seco-benzene system, and (±)-cicadamides E (6) and F (7), the NADA dimers derivatives, were isolated from Periostracum cicadae. The structures of all compounds were elucidated by spectroscopic analyses and computational methods. A plausible biosynthetic pathway for compounds 1-5 was proposed. The biological assay revealed that (+)-4 and (-)-4 exhibit renal protection in a dose-dependent manner.

Charting the Evolution of Chemoenzymatic Strategies in the Syntheses of Complex Natural Products

Bolstered by recent advances in bioinformatics, genetics, and enzyme engineering, the field of chemoenzymatic synthesis has enjoyed a rapid increase in popularity and utility. This Perspective explores the integration of enzymes into multistep chemical syntheses, highlighting the unique potential of biocatalytic transformations to streamline the synthesis of complex natural products. In particular, we identify four primary conceptual approaches to chemoenzymatic synthesis and illustrate each with a number of landmark case studies. Future opportunities and challenges are also discussed.

Skeletal diversification by C-C cleavage to access bicyclic frameworks from a common tricyclooctane intermediate

Herein, the diversification of tricyclo[3.2.1.03,6]octane scaffolds to afford diverse bicyclic scaffolds is described. The strained tricyclooctanes are prepared in two steps featuring a blue light-mediated [2+2] cycloaddition. Strategies for the cleavage of this scaffold were then explored resulting in the selective syntheses of the bicyclo[3.1.1]heptane, bicyclo[3.2.1]octane, and bicyclo[3.2.0]heptane cores. These findings may guide future studies of C-C cleavage reactions in strained carbon frameworks and their application in complex molecule synthesis.

Self-assembly and self-delivery of the pure nanodrug dihydroartemisinin for tumor therapy and mechanism analysis

Dihydroartemisinin (DHA), a plant-derived natural product, has recently been proven to be an effective therapeutic agent for cancer treatment. Nevertheless, the poor water solubility and low bioavailability of DHA seriously impede its clinical applications. Herein, a simple and green strategy based on the self-assembly of DHA was developed to synthesize carrier-free nanoparticles (NPs). The resulting nanodrug (DHA NPs) was formed by the self-assembly of DHA molecules via hydrogen bonding and hydrophobic interactions. The DHA NPs exhibited a near-spherical morphology with narrow size distribution, favorable drug encapsulation efficiency (>92%), excellent stability, and on-demand drug release behavior. Furthermore, the in vitro and in vivo experiments revealed that the DHA NPs exhibited significantly higher therapeutic efficacy than the DHA equivalent. In addition, we further explored the potential molecular mechanism of the DHA NPs by utilizing RNA-seq technology and western blotting analysis, which demonstrated that the p53 signaling pathway plays a crucial part in the process of inhibiting tumor cell growth and inducing apoptosis. This work not only reveals the rationale for developing pure nanodrugs via the self-assembly of natural small molecules for oncotherapy but also the investigation of the antitumor mechanism and provides novel theoretical support for the clinical usage of DHA.

New cytotoxic chalcone derivatives from Astragalus ponticus Pall

Astragalus ponticus Pall. species was investigated for its antiproliferative effects on HeLa cells. Two new chalcones (B5 and B8) along with eight known compounds (B1, B2, B3, B6, B7, B10, B14 and B15) were isolated by following bioactivity guided isolation methods. In addition, from non-active fraction, three cycloartane glycosides (B11, B12 and B13) were isolated. Molecular structures of these isolated compounds were revealed by using spectroscopic methods like MS, 1D and 2D NMR and a single crystal X-ray diffraction analysis. New compounds B5 and B8 showed the highest antiproliferative activities against HeLa cells (IC₅₀ values of 36.6 and 20.6 µM, respectively) while the rest showed high and low activities. Non-endemic species attract relatively low attention from the scientific community but this study demonstrates that valuable new compounds, which might be used as ingredients in medicinal preparations, can be obtained from these materials.

Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights

In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.

Self-assembled small molecule natural product gel for drug delivery: a breakthrough in new application of small molecule natural products

Natural products, as a gift of nature to humanity, have long been used as drugs or pharmacological actives to help people cure various diseases. Yet we still know comparatively little about their ability to be materials. In recent years, some small molecule natural products isolated from traditional Chinese medicines have been found to have new features, namely, self-assembly to form gels (i.e., natural product gels, NPG). However, the application development of these natural products is seriously lacking, which greatly weakens their practical value and delays the maturity of the field. Here, a series of self-assembled triterpenoid natural products are used as materials (gel scaffolds) to construct drug delivery systems. Surprisingly, these NPG not only exhibit the excellent self-healing, controlled gelation, good safety and sustained release, but also achieve synergistic treatment of tumors through bioactive natural products. Compared with non-bioactive gel scaffolds, NPG scaffolds show great advantages in tumor therapy, including optimal tumor inhibition, preferable health, better body recovery, stronger immune function, less toxic side effects and longer survival. The successful construction of NPG scaffolds not only takes full advantage of the self-assembled natural products, but also takes an important step in the development of new applications for natural products.

Targeted isolation of two disesquiterpenoid macrocephadiolides A and B from Ainsliaea macrocephala using a molecular networking-based dereplication strategy

Two novel dimeric sesquiterpenoids with potent anti-inflammatory activity were characterized from Ainsliaea macrocephala through a molecular networking-based dereplication strategy.

Total Synthesis as a Vehicle for Collaboration

"Collaboration" is not the first word most would associate with the field of total synthesis. In fact, the spirit of total synthesis is all-too-often reputed as being more competitive, rather than collaborative, sometimes even within individual laboratories. However, recent studies in total synthesis have inspired a number of collaborative efforts that strategically blend synthetic methodology, biocatalysis, biosynthesis, computational chemistry, and drug discovery with complex molecule synthesis. This Perspective highlights select recent advances in these areas, including collaborative syntheses of chlorolissoclimide, nigelladine A, artemisinin, ingenol, hippolachnin A, communesin A, and citrinalin B. The legendary Woodward-Eschenmoser collaboration that led to the total synthesis of vitamin B₁₂ is also discussed.

Marine Natural Products from Indonesian Waters

Natural products are primal and have been a driver in the evolution of organic chemistry and ultimately in science. The chemical structures obtained from marine organisms are diverse, reflecting biodiversity of genes, species and ecosystems. Biodiversity is an extraordinary feature of life and provides benefits to humanity while promoting the importance of environment conservation. This review covers the literature on marine natural products (MNPs) discovered in Indonesian waters published from January 1970 to December 2017, and includes 732 original MNPs, 4 structures isolated for the first time but known to be synthetic entities, 34 structural revisions, 9 artifacts, and 4 proposed MNPs. Indonesian MNPs were found in 270 papers from 94 species, 106 genera, 64 families, 32 orders, 14 classes, 10 phyla, and 5 kingdoms. The emphasis is placed on the structures of organic molecules (original and revised), relevant biological activities, structure elucidation, chemical ecology aspects, biosynthesis, and bioorganic studies. Through the synthesis of past and future data, huge and partly undescribed biodiversity of marine tropical invertebrates and their importance for crucial societal benefits should greatly be appreciated.

Marine-Derived Natural Compounds for the Treatment of Parkinson's Disease

Parkinson’s disease (PD) is a neurodegenerative disorder caused by the loss of dopaminergic neurons, leading to the motor dysfunctions of patients. Although the etiology of PD is still unclear, the death of dopaminergic neurons during PD progress was revealed to be associated with the abnormal aggregation of α-synuclein, the elevation of oxidative stress, the dysfunction of mitochondrial functions, and the increase of neuroinflammation. However, current anti-PD therapies could only produce symptom-relieving effects, because they could not provide neuroprotective effects, stop or delay the degeneration of dopaminergic neurons. Marine-derived natural compounds, with their novel chemical structures and unique biological activities, may provide anti-PD neuroprotective effects. In this study, we have summarized anti-PD marine-derived natural products which have shown pharmacological activities by acting on various PD targets, such as α-synuclein, monoamine oxidase B, and reactive oxygen species. Moreover, marine-derived natural compounds currently evaluated in the clinical trials for the treatment of PD are also discussed.

Self-assembled fibrillar networks induced by two methods: a new unmodified natural product gel

The discovery of new NPGs and the study of their self-assembing properties.

Harnessing the Properties of Natural Products

Natural products (NPs) have been used as traditional medicines since antiquity. With more than 10⁶⁰ estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments

The discovery of novel and/or new bioactive natural products from biota sources is often confounded by the reisolation of known natural products. Dereplication strategies that involve the analysis of NMR and MS spectroscopic data to infer structural features present in purified natural products in combination with database searches of these substructures provide an efficient method to rapidly identify known natural products. Unfortunately this strategy has been hampered by the lack of publically available and comprehensive natural product databases and open source cheminformatics tools. A new platform, DEREP-NP, has been developed to help solve this problem. DEREP-NP uses the open source cheminformatics program DataWarrior to generate a database containing counts of 65 structural fragments present in 229 358 natural product structures derived from plants, animals, and microorganisms, published before 2013 and freely available in the nonproprietary Universal Natural Products Database (UNPD). By counting the number of times one or more of these structural features occurs in an unknown compound, as deduced from the analysis of its NMR (¹H, HSQC, and/or HMBC) and/or MS data, matching structures carrying the same numeric combination of searched structural features can be retrieved from the database. Confirmation that the matching structure is the same compound can then be verified through literature comparison of spectroscopic data. This methodology can be applied to both purified natural products and fractions containing a small number of individual compounds that are often generated as screening libraries. The utility of DEREP-NP has been verified through the analysis of spectra derived from compounds (and fractions containing two or three compounds) isolated from plant, marine invertebrate, and fungal sources. DEREP-NP is freely available at https://github.com/clzani/DEREP-NP and will help to streamline the natural product discovery process.

Structurally Diverse Alkaloids from the Seeds of Peganum harmala

Investigation of the alkaloids from Peganum harmala seeds yielded two pairs of unique racemic pyrroloindole alkaloids, (±)-peganines A-B (1-2); two rare thiazole derivatives, peganumals A-B (3-4); six new β-carboline alkaloids, pegaharmines F-K (5-10); and 12 known analogues. Their structures, including stereochemistry, were elucidated through spectroscopic analyses, quantum chemistry calculations, and single-crystal X-ray diffraction. Notably, the incorporation of pyrrole and indole moieties in peganines A-B, thiazole fragments in peganumals A-B, and a C-1 α,β-unsaturated ester motif in pegaharmine F (5) are all rare, and their presence in the genus Peganum were demonstrated for the first time. All isolates were tested for antiproliferative activities against the HL-60, PC-3, and SGC-7901 cancer cell lines, and compounds 9, 11, 12, and 13 exhibited moderate cytotoxicity against HL-60 cancer cell lines with IC₅₀ values in the range of 4.36-9.25 μM.

Natural diarylfluorene derivatives: isolation, total synthesis, and phosphodiesterase-4 inhibition

The first total synthesis of selaginpulvilins A–F and evaluation of their PDE4 inhibitory activities.

New p-terphenyls from the endophytic fungus Aspergillus sp. YXf3

Five new p-terphenyls named prenylterphenyllin D (1), prenylterphenyllin E (2), 2'-O-methylprenylterphenyllin (3), 4-O-methylprenylterphenyllin (4) and 3'-O-methylterphenyllin (5) together with seven known compounds (6-12), were isolated from cultures of Aspergillus sp. YXf3. The structures of the new compounds were elucidated by extensive MS and NMR analyses. The NMR and MS data of 5 is reported for the first time, as its structure was listed in SciFinder Scholar with no associated reference. Compounds 6 and 7 were distinguished from each other on the basis of 2D NMR experiments. Compounds 1, 2, 3 and 8 showed antibacterial activities against X. oryzae pv. oryzicola Swings and E. amylovora with the same MIC values of 20μg/mL while 10 exhibited activities against E. amylovora with an MIC value of 10μg/mL.

A Series of β-Carboline Alkaloids from the Seeds of Peganum harmala Show G-Quadruplex Interactions

In this study, we screened 17 medicinal plants for binding activity to G-quadruplex d(TTGGGTT)4 by (1)H NMR spectroscopy and found that the crude extract of Peganum harmala L. seeds showed the most potential binding activity. Subsequently, (1)H NMR- and bioassay-guided isolation of the extract of P. harmala L. was performed to obtain four pairs of partially racemized β-carboline alkaloids, pegaharmines A-D (1-4). Their structures and absolute configurations were determined by extensive NMR analyses, X-ray crystallography, ECD calculations, and CD exciton chirality approaches. Interestingly, pegaharmine D (4), which showed the strongest G-quadruplex interaction, exhibited significant cytotoxic activity against three cancer cell lines. This work contributed a practical strategy for the discovery of novel G-quadruplex ligands from natural products and provided potential insights for using β-carboline alkaloids as anticancer lead compounds specifically targeting G-quadruplexes.

Total Synthesis, Stereochemical Revision, and Biological Reassessment of Mandelalide A: Chemical Mimicry of Intrafamily Relationships

Mandelalide A and three congeners had recently been isolated as the supposedly highly cytotoxic principles of an ascidian collected off the South African coastline. Since these compounds are hardly available from the natural source, a concise synthesis route was developed, targeting structure 1 as the purported representation of mandelalide A. The sequence involves an iridium-catalyzed two-directional Krische allylation and a cobalt-catalyzed carbonylative epoxide opening as entry points for the preparation of the major building blocks. The final stages feature the first implementation of terminal acetylene metathesis into natural product total synthesis, which is remarkable in that this class of substrates had been beyond the reach of alkyne metathesis for decades. Synthetic 1, however, proved not to be identical with the natural product. In an attempt to clarify this issue, NMR spectra were simulated for 20 conceivable diastereomers by using DFT followed by DP4 analysis; however, this did not provide a reliable assignment either. The puzzle was ultimately solved by the preparation of three diastereomers, of which compound 6 proved identical with mandelalide A in all analytical and spectroscopic regards. As the entire "northern sector" about the tetrahydrofuran ring in 6 shows the opposite configuration of what had originally been assigned, it is highly likely that the stereostructures of the sister compounds mandelalides B-D must be corrected analogously; we propose that these natural products are accurately represented by structures 68-70. In an attempt to prove this reassignment, an entry into mandelalides C and D was sought by subjecting an advanced intermediate of the synthesis of 6 to a largely unprecedented intramolecular Morita-Baylis-Hillman reaction, which furnished the γ-lactone derivative 74 as a mixture of diastereomers. Whereas (24R)-74 was amenable to a hydroxyl-directed dihydroxylation by using OsO4 /TMEDA as the reagent, the sister compound (24S)-74 did not follow a directed path but simply obeyed Kishi's rule; only this unexpected escape precluded the preparation of mandelalides C and D by this route. A combined spectroscopic and computational (DFT) study showed that the reasons for this strikingly different behavior of the two diastereomers of 74 are rooted in their conformational peculiarities. This aspect apart, our results show that the OsO4 /TMEDA complex reacts preferentially with electron deficient double bonds even if other alkenes are present that are more electron rich and less encumbered. Finally, in a brief biological survey authentic mandelalide A (6) was found to exhibit appreciable cytotoxicity only against one out of three tested human cancer cell lines and all synthetic congeners were hardly active. No significant fungicidal properties were observed.

Muta-mycosynthesis of naphthalene analogs

A mutasynthetic strategy is introduced for the mycosynthesis of naphthalene-based molecules (mutadalesols A-F) with directed substitution patterns and new frameworks by generating and using the ΔpksTL mutant strain of Daldinia eschscholzii. (±)-Mutadalesol A and its (+)-enantiomer are cytotoxic, and its (-)-enantiomer inhibits Toll-like receptor 5 (TLR5). The in-culture reactability of fungal oligoketide intermediates with 5-aminonaphthalen-1-ol (ANL) is demonstrated, shedding light on bioorthogonal accesses to unnatural molecule libraries valuable in drug discovery pipelines.

Pictet-Spengler reaction-based biosynthetic machinery in fungi

The Pictet-Spengler (PS) reaction constructs plant alkaloids such as morphine and camptothecin, but it has not yet been noticed in the fungal kingdom. Here, a silent fungal Pictet-Spenglerase (FPS) gene of Chaetomium globosum 1C51 residing in Epinephelus drummondhayi guts is described and ascertained to be activable by 1-methyl-L-tryptophan (1-MT). The activated FPS expression enables the PS reaction between 1-MT and flavipin (fungal aldehyde) to form "unnatural" natural products with unprecedented skeletons, of which chaetoglines B and F are potently antibacterial with the latter inhibiting acetylcholinesterase. A gene-implied enzyme inhibition (GIEI) strategy has been introduced to address the key steps for PS product diversifications. In aggregation, the work designs and validates an innovative approach that can activate the PS reaction-based fungal biosynthetic machinery to produce unpredictable compounds of unusual and novel structure valuable for new biology and biomedicine.