Modification Of Natural Products Research Articles

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.

Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developedlineagespecificanalysis of BGCs (lsaBGC;https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest.lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin inStaphylococcus aureusis ubiquitous across the genusStaphylococcus. While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associatedStaphylococcus. Further, the latter GCF, which is well conserved inS. aureus, has been lost in mostStaphylococcus epidermidis, which is the most commonStaphylococcusspecies on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from theCorynebacterium tuberculostearicumsp. complex, a narrow, multi-species clade that features the most prevalentCorynebacteriumin healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites,lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs,lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.

Optimization of Osthole in the Lactone Ring as an Agrochemical Candidate: Synthesis, Characterization, and Pesticidal Activities of Osthole Amide/Ester Derivatives and Their Effects on Morphological Changes of Mite Epidermis

Structural modification of natural products is one of the important ways in the discovery of novel pesticides. Based on a diversity-oriented synthesis strategy, herein, two series of amide/ester derivatives (52 compounds) were obtained by opening the lactone of osthole. Interestingly, the effect of different concentrations of aq. sodium hydroxide on the ratio of two isomers (cis- and trans-2) was investigated, and a magical phenomenon of ultraviolet (UV) light irradiation on intertransformation of two isomers (cis- and trans-2) was observed. Against Mythimna separata, when compared with the precursor osthole, compounds 4b, 4l, 5l, 5m, 7h, 7l, and 7m displayed more pronounced growth inhibitory activity with the final mortality rates of 62.0-68.9%. Compounds 4b, 4i, and 5m showed 5.7-6.6 times stronger acaricidal activity against Tetranychus cinnabarinus than osthole, and notably, control effects of compounds 4i and 5m were 2.4- and 2.7-fold that of osthole in the management of T. cinnabarinus in the greenhouse. Scanning electron microscopy (SEM) images of the epidermis of 5m-treated T. cinnabarinus indicated that compound 5m can destroy the mite cuticle layer. Compounds 4b and 5m can be used as leads to further explore more promising pesticidal agents.

Stereoselective C–O silylation and stannylation of alkenyl acetates

Facile formation of carbon-heteroatom bonds is a long-standing objective in synthetic organic chemistry. However, direct cross-coupling with readily accessible alkenyl acetates via inert C‒O bond-cleavage for the carbon-heteroatom bond construction remains challenging. Here we report a practical preparation of stereoselective tri- and tetrasubstituted alkenyl silanes and stannanes by performing cobalt-catalyzed C‒O silylation and stannylation of alkenyl acetates using silylzinc pivalate and stannylzinc chloride as the nucleophiles. This protocol features a complete control of chemoselectivity, stereoselectivity, as well as excellent functional group compatibility. The resulting alkenyl silanes and stannanes show high reactivities in arylation and alkenylation by Hiyama and Stille reactions. The synthetic utility is further illustrated by the facile late-stage modifications of natural products and drug-like molecules. Mechanistic studies suggest that the reaction might involve a chelation-assisted oxidative insertion of cobalt species to C‒O bond. We anticipate that our findings should prove instrumental for potential applications of this technology to organic syntheses and drug discoveries in medicinal chemistry.

Photocatalytic deconstructive aliphatic carbon–carbon bond cleavage and functionalization of unactivated alcohols

Carbon–carbon (C–C) bonds are challenging to selectively cleave owing to their chemical inertness and omnipresence in organic molecules; however, they can be targeted during the late-stage modification of natural products and active pharmaceutical ingredients. Herein, we report a selective deconstructive C(sp3)–C(sp3) bond cleavage and difunctionalization of unactivated alcohols mediated by a vanadium visible-light photocatalyst under ambient temperatures and pressures. Our base metal photocatalyst operates via ligand-to-metal charge transfer followed by an inner-sphere C–C bond cleavage to generate alkyl radicals that are trapped with SOMOphiles. We achieved 10 different bond formations on 44 examples using a range of commercially sourced alcohols, including natural products and biomolecules. Our protocol can also be used for the regio- and diastereoselective cyclization to form an α-aminolactone, and for the late-stage functionalization of bioactive oligopeptides to access unnatural amino acid residues.

Recent updates in click and computational chemistry for drug discovery and development.

Drug discovery is a costly and time-consuming process with a very high failure rate. Recently, click chemistry and computer-aided drug design (CADD) represent popular areas for new drug development. Herein, we summarized the recent updates in click and computational chemistry for drug discovery and development including clicking to effectively synthesize druggable candidates, synthesis and modification of natural products, targeted delivery systems, and computer-aided drug discovery for target identification, seeking out and optimizing lead compounds, ADMET prediction as well as compounds synthesis, hopefully, inspires new ideas for novel drug development in the future.

Isoxazole/Isoxazoline Skeleton in the Structural Modification of Natural Products: A Review.

Isoxazoles and isoxazolines are five-membered heterocyclic molecules containing nitrogen and oxygen. Isoxazole and isoxazoline are the most popular heterocyclic compounds for developing novel drug candidates. Over 80 molecules with a broad range of bioactivities, including antitumor, antibacterial, anti-inflammatory, antidiabetic, cardiovascular, and other activities, were reviewed. A review of recent studies on the use of isoxazoles and isoxazolines moiety derivative activities for natural products is presented here, focusing on the parameters that affect the bioactivity of these compounds.

Copper-Catalyzed C2- or C3-Thioglycosylation of Indoles with N-(Thioglycosides)succinimides: An Effective Strategy for the Total Synthesis of Isatindigotindolosides.

Isatindigotindolosides, indoles containing a 1-S-β-glucopyranosyl unit at position C2, show promising bioactivity. Here, we report a copper-catalyzed C2- or C3-thioglycosylation of indoles with N-(thioglycosides)succinimides to construct indole alkaloid glucosides. This reaction is widely tolerant of functional groups, as various indoles and thioglycosides are suitable. It also provides a reliable method for performing late-stage modifications of natural products, such as gramine and melatonin. Total syntheses of isatindigotindolosides I and II were successfully accomplished using the C2-thioglycosylation reaction as a key step.

A novel class of C14-sulfonate-tetrandrine derivatives as potential chemotherapeutic agents for hepatocellular carcinoma.

Hepatocellular carcinoma (HCC), the most common malignancy of the liver, exhibits high recurrence and metastasis. Structural modifications of natural products are crucial resources of antitumor drugs. This study aimed to synthesize C-14 derivatives of tetrandrine and evaluate their effects on HCC. Forty C-14 sulfonate tetrandrine derivatives were synthesized and their in vitro antiproliferative was evaluated against four hepatoma (HepG-2, SMMC-7721, QGY-7701, and SK-Hep-1) cell lines. For all tested cells, most of the modified compounds were more active than the lead compound, tetrandrine. In particular, 14-O-(5-chlorothiophene-2-sulfonyl)-tetrandrine (33) exhibited the strongest antiproliferative effect, with half-maximal inhibitory concentration values of 1.65, 2.89, 1.77, and 2.41μM for the four hepatoma cell lines, respectively. Moreover, 33 was found to induce apoptosis via a mitochondria-mediated intrinsic pathway via flow cytometry and western blotting analysis. In addition, colony formation, wound healing, and transwell assays demonstrated that 33 significantly inhibited HepG-2 and SMMC-7721 cell proliferation, migration, and invasion, indicating that it might potentially be a candidate for an anti-HCC therapy in the future.

C-H modification of natural products: a minimalist enabling tactic for drug discovery, API processing and bioconjugation.

Intrusion into the C-H chemical space of natural products through the strategic deployment of C-H functionalization reactions could lead to incredibly new molecular diversities with an unforeseen impact on biological functions. Based on this hypothesis, semisynthetic C-H modification of natural products is emerging as a minimalist tactic in natural product based drug discovery. Several examples of C-H modification of natural products, resulting in functional gains in key pharmacological attributes viz. potency, aqueous solubility and DMPK profile, along with opportunities in allied areas such as API processing, bioconjugation, and target deconvolution, continue to surface in the recent literature. The strategy has already recorded commercial success in the development of antineoplastic drugs topotecan and irinotecan and in industrial production of pravastatin, calcitriol and artemisinin. This Feature Article highlights the broad contours of this evolving paradigm at the interface of natural product and synthetic chemistry research to accelerate and widen the scope of natural product-based drug discovery.

Potential anticancer and antioxidant lauric acid-based hydrazone synthesis and computational study toward the electronic properties.

The modification of natural products is one of the key areas of synthetic organic chemistry for obtaining valuable chemical building blocks that have medicinal significance. In this study, lauric acid-based hydrazones, namely (E)-N'-(2-nitrobenzylidene)dodecanehydrazide (NBDH), (E)-N'-(naphthalen-1-ylmethylene)dodecanehydrazide (NMDH), and (E)-N'-(4-fluorobenzylidene)dodecanehydrazide (FBDH), were synthesized and characterized using spectroscopic techniques. The newly synthesized lauric acid-based hydrazones were screened for their anticancer and antioxidant potential. The antioxidants showed their activity by inhibiting the oxidative chain reactions that produce reactive oxygen species. The antioxidant activity showed that NBDH exhibited the maximum DPPH inhibitory activity when compared with that of NMDH and FBDH, whereas the anticancer activity showed that FBDH exhibited maximum percent viability when compared to that of NBDH and NMDH. The reactivity and biological needs of the synthesized compounds NBDH, NMDH, and FBDH were met by performing geometrical, FT-IR vibrational, UV-visible, global reactivity parameters (GRP), MEP, FMO, NBO, ELF, LOL, and nonlinear optical (NLO) analysis at the DFT/B3LYP/6-311+G(d,p) level. NBO analysis confirmed the existence of extended conjugation and intramolecular charge transfer among NBDH, NMDH, and FBDH, which have the lowest gap in π → π*, which are in line with the FMO results where successful charge transfer occurred from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO). GRP analysis confirmed the potential of NBDH, NMDH, and FBDH for biological, electronic, and NLO applications. It is clear from the comparative analysis of the urea molecule that NBDH, NMDH, and FBDH all comprise fine NLO properties.

Functional analysis of a fungal P450 enzyme.

Fungal cytochrome P450s participate in various physiological reactions, including the synthesis of internal cellular components, metabolic detoxification of xenobiotic compounds, and oxidative modification of natural products. Although functional analysis reports of fungal P450s continue to grow, there are still some difficulties as compared to prokaryotic P450s, because most of these fungal enzymes are transmembrane proteins. In this chapter, we will describe the methods for heterologous expression, in vivo analysis, enzyme preparation, and in vitro enzyme assays of the fungal P450 enzyme Trt6 and isomerase Trt14, which play important roles in the divergence of the biosynthetic pathway of terretonins, as a model for the functional analysis of fungal P450 enzymes.

Palladium-Catalyzed Domino Reaction for the Assembly of Norbornane-Containing Chromones with Dimethyl Squarate as the Solid C1 Source.

Reported herein is a novel palladium-catalyzed [2 + 2 + 1] domino annulation of 3-iodochromones, bridged olefins, and dimethyl squarate allowing the construction of chromone-containing polycyclic compounds in good to high yields. Importantly, dimethyl squarate is first employed as the solid C1 source in organic synthesis. Gram-scale experiments, late-stage modification of natural products, as well as transformations of products show potential for further synthetic elaborations.

Three-Component Perfluoroalkylvinylation of Alkenes Enabled by Dual DBU/Fe Catalysis.

Herein, a simple and efficient strategy that involves dual 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)/iron-catalyzed alkene perfluoroalkylvinylation by using perfluoroalkyl iodides and 2-aminonaphthalene-1,4-diones as coupling partners is demonstrated. In terms of the developed catalytic system, various styrenes and aliphatic alkenes are well-tolerated, leading to the accurate preparation of perfluoroalkyl-containing 2-aminonaphthalene-1,4-diones in excellent regioselectivity. Moreover, the protocol can be readily applied in late-stage modifications of natural products and pharmaceuticals. The title reactions are featured by easily accessible and inexpensive catalysts and substrates, broad substrate applicability, and mild reaction conditions. Mechanistic investigations reveal a tandem C-I cleavable alkylation and C-C vinylation enabled by cooperative DBU/iron catalysis.

Design, Synthesis and Fungicidal Activity of N-(thiophen-2-yl) Nicotinamide Derivatives

Based on the modification of natural products and the active substructure splicing method, a series of new N-(thiophen-2-yl) nicotinamide derivatives were designed and synthesized by splicing the nitrogen-containing heterocycle natural molecule nicotinic acid and the sulfur-containing heterocycle thiophene. The structures of the target compounds were identified through 1H NMR, 13C NMR and HRMS spectra. The in vivo bioassay results of all the compounds against cucumber downy mildew (CDM, Pseudoperonospora cubensis (Berk.et Curt.) Rostov.) in a greenhouse indicated that compounds 4a (EC50 = 4.69 mg/L) and 4f (EC50 = 1.96 mg/L) exhibited excellent fungicidal activities which were higher than both diflumetorim (EC50 = 21.44 mg/L) and flumorph (EC50 = 7.55 mg/L). The bioassay results of the field trial against CDM demonstrated that the 10% EC formulation of compound 4f displayed excellent efficacies (70% and 79% control efficacies, respectively, each at 100 mg/L and 200 mg/L) which were superior to those of the two commercial fungicides flumorph (56% control efficacy at 200 mg/L) and mancozeb (76% control efficacy at 1000 mg/L). N-(thiophen-2-yl) nicotinamide derivatives are significant lead compounds that can be used for further structural optimization, and compound 4f is also a promising fungicide candidate against CDM that can be used for further development.

CFNC, a neocryptolepine derivative, inhibited the growth of gastric cancer AGS cells by inhibiting PI3K/AKT signaling pathway

Gastric cancer is highly heterogeneous and there is still a lack of efficient, low-toxicity small molecule compounds for the treatment of gastric cancer. Natural products are important sources for the development of antitumor compounds. Therefore, it is promising strategy to find the lead compound of anti-gastric cancer agents by structural modification of natural products. The aim of this study was to synthesize a novel neocryptolepine derivative CFNC and explore its potential anti-gastric cancer effect and molecular mechanism. The MTT assay showed that the IC50 of CFNC on AGS cells reached 148 nM. CFNC arrested AGS cells in the G2/M phase of the cell cycle. Furthermore, CFNC inhibited cell proliferation and migration, leading to the loss of membrane potential by causing mitochondrial dysfunction, which induced the apoptosis of AGS cells. Western blot assay suggested that CFNC could inhibit the expression of important proteins in the PI3K/AKT/mTOR signaling pathway. These results showed that CFNC exhibited strong cytotoxic activity in gastric cancer cell lines by regulating the PI3K/AKT/mTOR signaling pathway. Taken together, CFNC could be a promising lead compound for the clinical treatment of gastric cancer.

Two-enzyme cascade catalyzed trideuteromethylative modification of natural products

Site-selective incorporation of the trideuterated “magic methyl” group may provide profound pharmacological benefits, which has been considered as an important tool for drug optimization and development in medicinal chemistry. S-adenosyl-L-methionine (SAM) usually acts as the methyl donor under the catalysis of SAM-dependent methyltransferases (MTs), which transfer a methyl group from SAM to substrates, and are widely reported for methylation in natural product biosynthesis. However, it is difficult to introduce other high-value functional groups to substrates in this way since SAM analogs are not easy to obtain in biological methods. Herein we report that trideuterated SAM can be obtained from S-adenosylhomocysterine (SAH) and trideuterated methyl iodide (CD3I) under the participation of halide methyltransferase (HMT). Subsequent one-pot cascades with different MTs achieved the regioselective trideuteromethylation of three natural products, which indicated that trideuterated SAM can be accepted as a co-substrate by C-, N-, O-specific MTs for enzyme-catalyzed trideuteromethylation of natural products.

Genome editing technologies, mechanismsand improved production of therapeutic phytochemicals: Opportunities and prospects.

Plants produce a large number of secondary metabolites, known as phytometabolites that may be employed as medicines, dyes, poisons, and insecticides in the field of medicine, agriculture, and industrial use, respectively. The rise of genome management approaches has promised a factual revolution in genetic engineering. Targeted genome editing in living entities permits the understanding of the biological systems very clearly, and also sanctions to address a wide-ranging objective in the direction of improving features of plant and their yields. The last few years have introduced a number of unique genome editing systems, including transcription activator-like effector nucleases, zinc finger nucleases, and miRNA-regulated clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). Genome editing systems have helped in the transformation of metabolic engineering, allowing researchers to modify biosynthetic pathways of different secondary metabolites. Given the growing relevance of editing genomes in plant research, the exciting novel methods are briefly reviewed in this chapter. Also, this chapter highlights recent discoveries on the CRISPR-based modification of natural products in different medicinal plants.

Catalyst-Free C(sp2)-H Borylation through Aryl Radical Generation from Thiophenium Salts via Electron Donor-Acceptor Complex Formation.

Aryl borates lie at the heart of carbon-carbon bond couplings, and they are widely applied to the synthesis of functional materials, pharmaceutical compounds, and natural products. Currently, synthetic methods for aryl borates are mostly limited to metal-catalyzed routes, and nonmetallic strategies remain comparatively underdeveloped. Herein, we report a mild, scalable, visible-light-induced cross-coupling between aryl dibenzothiophenium triflate salts and bis(catecholato)-diboron for the construction of C-B bonds in the absence of base, transition metal-ligand complex, or photoredox catalyst. Mechanistic studies reveal that this transformation is achieved through an electron donor-acceptor (EDA) complex activation in the absence of a catalyst. The mild reaction conditions allow the preparation of aromatic borates in good yields with excellent functional group tolerance. This photochemical protocol was also successfully applied to the late-stage modification of natural products and the synthesis of a drug intermediate, greatly demonstrating broadened utility.

Discovery of 29-O-acyl-toosendanin-based derivatives as potent anti-cancer agents

Structural modification of natural products is an effective strategy to discover potent lead compounds with improved medicinal performance. Toosendanin (TSN), a natural limonoid with diverse pharmacological properties, was selected as the starting material for structural modification to obtain more active anti-cancer agents in the current study. A library containing 25 structurally diverse derivatives (including 12 new ones) were constructed on the basis of the structure-guided modification of TSN. Subsequent cytotoxic assay of this library discovered that compounds 14, 18, and 25 showed more significant antiproliferative activity than the precursor TSN in MDA-MB-468 cell model and so as compounds 14, 17–19, 21, and 25 in Hela cell model. Among them, the new derivative 29-O-(6-chloronicotinoyl)-toosendanin (25) exhibited the most potent antiproliferative activity (IC50s 0.05–0.06 μM), being more active than TSN (IC50s 0.14–0.24 μM) and even the first-line drug adriamycin (IC50s ∼ 0.07 μM) in both tested cancer cell lines. The SARs study uncovered that the hemiacetal group, the 14,15-epoxy ring, 1-OH, 7-OH, 3-OAc, and 12-OAc were viewed as the essential active groups and the 29-OH was the critically active modification position of TSN for the enhancement of cytotoxicity. The discovering of 25 from TSN-based derivatives might serve as a lead compound for anti-cancer chemotherapy, which may shed light on rationally design TSN-based derivatives for obtaining more potent anti-tumor agents.

Radical Hydro‐Fluorosulfonylation of Unactivated Alkenes and Alkynes

AbstractRecently, radical fluorosulfonylation is emerging as an appealing approach for the synthesis of sulfonyl fluorides, which are highly in demand in various disciplines, particularly in chemical biology and drug discovery. Here, we report the first establishment of radical hydro‐fluorosulfonylation of alkenes, which is enabled by using 1‐fluorosulfonyl 2‐aryl benzoimidazolium (FABI) as an effective redox‐active radical precursor. This method provides a new and facile approach for the synthesis of aliphatic sulfonyl fluorides from unactivated alkenes, and can be further applied to the late‐stage modifications of natural products and peptides, as well as ligation of drugs in combination with click chemistry. Remarkably, this system could enable the radical hydro‐fluorosulfonylation of alkynes, affording valuable alkenylsulfonyl fluoride products with a rare, highZ‐selectivity, which are normally less stable and more challenging to synthesize in comparison with theE‐configured products.