Natural Product Scaffolds Research Articles

The use of natural product scaffolds as leads in the search for trypanothione reductase inhibitors

Twenty-three heterocyclic compounds were evaluated for their potential as trypanothione reductase inhibitors. As a result, the harmaline, 10-thiaisoalloxazine, and aspidospermine frameworks were identified as the basis of inhibitors of Trypanosoma cruzi trypanothione reductase. Two new compounds showed moderately strong, linear competitive inhibition, namely N, N-dimethyl- N-[3-(7-methoxy-1-methyl-3,4-dihydro-9 H-β-carbolin-9-yl)propyl]amine ( 15) and 1,3-bis[3-(dimethylamino)propyl]-1,5-dihydro-2 H-pyrimido[4,5- b][1,4]benzothiazine-2,4(3 H)-dione ( 21), with K i values of 35.1 ± 3.5 μM and 26.9 ± 1.9 μM, respectively. Aspidospermine ( 25) inhibited T. cruzi TryR with a K i of 64.6 ± 6.2 μM. None of the compounds inhibited glutathione reductase. Their toxicity toward promastigotes of Leishmania amazonensis was assessed.

Evolution of Natural Product Scaffolds by Acyl- and Arylnitroso Hetero-Diels−Alder Reactions: New Chemistry on Piperine

Piperine, a natural product containing a conjugated diene, was reacted with polymer-supported acyl- and arylnitroso dienophiles. The reactions with arylnitroso dienophiles were also carried out in solution. The oxazine rings formed by the corresponding hetero-Diels-Alder reactions were further transformed and novel acyclic as well as heterocyclic derivatives including pyrroles and quinoxalinones were prepared.

Anti-MRSA agent discovery using diversity-oriented synthesis.

Antibacterial drugs have played an essential role in the global increase in quality of life and life expectancy. However, these gains are at serious risk owing to bacterial drug resistance by so-called “superbugs”, such as methicillin-resistant Staphylococcus aureus (MRSA). The discovery of new antibiotics with novel modes of action is vital to tackle the threat of multidrug-resistant bacteria. Traditionally, antibiotics have been discovered from natural sources; however, there are many disadvantages to using extracts (e.g. limited availability, bioactive constituent identification, and complex analogue synthesis). These problems have led to a complementary approach of synthesizing structurally diverse, natural-product-like small molecules directly and efficiently, an approach known as diversity-oriented synthesis (DOS). Whereas compound collections of a common scaffold decorated with diverse building blocks have been synthesized efficiently, there are limited examples of the synthesis of small molecules with a high degree of skeletal diversity (usually by a build–couple–pair strategy). Previously, we have used a diazoacetate starting unit to mimic nature8s divergent synthetic strategy with acetyl CoA (by a pluripotent functional-group strategy) to synthesize compounds with natural-product scaffolds (e.g. cocaine and warfarin). Herein, we report the use of a solid-supported phosphonate unit to synthesize 242 drug-like compounds based on 18 natural-product-like scaffolds in two to five steps and their use in discovering a new structural class of antibiotic with anti-MRSA activity. The solid-supported phosphonate 1 (Scheme 1) was identified as an attractive DOS starting unit for three key reasons. First, the reactive phosphonate functionality permits the stereoselective formation of a,b-unsaturated acyl imidazolidinones (2) that could be used to generate enantioselectively a wide range of scaffolds that can be diversified further. Second, the imidazolidinone linker not only enables twopoint binding of chiral catalysts but also permits divergent cleavage of the exocyclic acyl group (hydrolysis, reduction, esterification, and amide formation). Thirdly, immobilization of 1 on a silyl polystyrene support simplified reaction optimization and work-up procedures in the multistep parallel synthesis (total of over 1000 individual steps), thereby allowing the efficient production of milligram quantities of 242 compounds without the requirement for automation equipment. In the first step of the diversity-oriented synthesis, 1 was treated with aldehyde building blocks (aryl, heteroaryl, and alkyl; see the Supporting Information) to deliver twelve a,bunsaturated acyl imidazolidinones (2). The second steps of the solid-supported synthesis exploited three catalytic, enantioselective, divergent reaction pathways (Scheme 1): 1) [2+3] cycloaddition (reaction b, ee 60–65%, de 7899%), 2) dihydroxylation (reaction c, ee 88–91%), and 3) [4+2] cycloaddition (reaction d, ee 89–98%, de 74– 74%). Similar selectivities were observed when repeating the reactions in solution with a triisopropylsilyl-protected linker (as opposed to the diisopropylpolystyrene group; see the Supporting Information). The reactions were also conducted with achiral catalysts to give racemic products, which were used for the later steps of the synthesis. This procedure enabled the diversity-oriented synthesis to be streamlined to half the size, yet permitted the enantioselective synthesis of hits during the structure–activity relationship stages of this [*] Dr. G. L. Thomas, R. J. Spandl, F. G. Glansdorp, Dr. M. Ladlow, Dr. D. R. Spring Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK) Fax: (+44) 1223-336362 E-mail: drspring@ch.cam.ac.uk Homepage: http://www-spring.ch.cam.ac.uk/

Unraveling the molecular targets of natural products: Insights from genomic and proteomic analyses

Natural products and their derivatives have been an invaluable source of drug leads for the pharmaceutical industry over the past decades, especially for antibacterial and anticancer purposes. Nature products, with their chemical diversity and biochemical specificity, are ideal starting points of drug development. Rational drug design based on natural product scaffolds, however, was hindered by a lack of knowledge regarding their mechanisms of action. Advances in proteomic technologies hold the key to revolutionize the target identification of natural products. In this regard, chemical proteomics have demonstrated the capabilities to identify specific targets by screening against the proteome. On the other hand, high-throughput proteome analysis reveals the multiple impacts of drug-target interaction in a global context, providing insights for elucidation of signaling pathways involved in the drug response, and uncovering predictive markers of drug efficacy and toxicity. Increasingly, studies have exploited integration of transcriptome and proteome datasets, which offers additional information on regulation of molecular network at transcriptional and post-translational levels. In this review, we discuss major proteomic approaches applied to studying the mechanism of action of natural products and merits of combining datasets from proteomics and transcriptomics analysis.

Biocatalytic and semisynthetic optimization of the anti-invasive tobacco (1 S,2 E,4 R,6 R,7 E,11 E)-2,7,11-cembratriene-4,6-diol

Tobacco cembranoids were reported to inhibit tumorigenesis. Biocatalysis of (1 S,2 E,4 R,6 R,7 E,11 E)-2,7,11-cembratriene-4,6-diol ( 1) using the symbiotic Bacillus sp. NC5, Bacillus sp. NK8, and Bacillus sp. NK7, isolated from the Red Sea sponge Negombata magnifica, afforded two new and four known hydroxylated metabolites 3– 8. The use of symbiotic marine bacteria as biocatalysts for bioactive natural product scaffolds is very rare. Cembranoid 1 carbamate analogs 9– 11 were prepared by its reaction with corresponding isocyanates. Cembranoid 1 and its bioconversion and carabamate products show anti-invasive activity against the human highly metastatic prostate PC-3M cancer cell line at 10–50 nM doses in Matrigel assay.

Engineered biosynthesis of hybrid macrolide polyketides containing d-angolosamine and d-mycaminose moieties

The glycosylation of natural product scaffolds with highly modified deoxysugars is often essential for their biological activity, being responsible for specific contacts to molecular targets and significantly affecting their pharmacokinetic properties. In order to provide tools for the targeted alteration of natural product glycosylation patterns, significant strides have been made to understand the biosynthesis of activated deoxysugars and their transfer. We report here efforts towards the production of plasmid-borne biosynthetic gene cassettes capable of producing TDP-activated forms of D-mycaminose, D-angolosamine and D-desosamine. We additionally describe the transfer of these deoxysugars to macrolide aglycones using the glycosyl transferases EryCIII, TylMII and AngMII, which display usefully broad substrate tolerance.

Desymmetrization of 7-azabicycloalkenes by tandem olefin metathesis for the preparation of natural product scaffolds

BackgroundTandem olefin metathesis sequences are known to be versatile for the generation of natural product scaffolds and have also been used for ring opening of strained carbo- and heterocycles. In this paper we demonstrate the potential of these reactions for the desymmetrization of 7-azabicycloalkenes.ResultsWe have established efficient protocols for the desymmetrization of different 7-azabicycloalkenes by intra- and intermolecular tandem metathesis sequences with ruthenium based catalysts.ConclusionDesymmetrization of 7-azabicycloalkenes by olefin metathesis is an efficient process for the preparation of common natural product scaffolds such as pyrrolidines, indolizidines and isoindoles.

Derrubone, an Inhibitor of the Hsp90 Protein Folding Machinery

High-throughput screening of a library of diverse molecules has identified derrubone ( 1), an isoflavone natural product from Derris robusta, as a potent Hsp90 inhibitor. Subsequent testing in several cellular-based assays established 1 as a low micromolar inhibitor in vitro. In addition, derrubone induced the degradation of numerous Hsp90 client proteins, a hallmark effect resulting from Hsp90 inhibition. The identification of 1 as an Hsp90 inhibitor provides a new natural product scaffold upon which the development of novel Hsp90 inhibitors can be pursued.

Asymmetric Rhodium-Catalyzed [4+3] Cycloaddition

A novel methodology for the asymmetric synthesis of tropanes (a popular natural product scaffold) is described using a rhodium-catalyzed [4+3] cycloaddition between pyrroles and a vinyldiazoacetate. The reaction tolerates a wide range of substituted pyrroles with good yields and excellent enantioselectivities. The products can be an intermediate or a precursor to an intermediate in several previously reported syntheses of biologically active tropanes.

An efficient one-pot synthesis of tethered cyclohexadiene enaminonitriles from methyl-ketones: An effective route to quinazolines

The quinazolines represent a useful natural product scaffold with demonstrated activities against disorders such as high blood pressure and benign prostatic hyperplasia. Here we report on the synthesis and biological activity of a series of quinazolines that were prepared by a one-pot synthesis of substituted cyclohexadiene enaminonitriles from methyl-ketones. The approach, which employs NaH, complements published procedures where LDA is utilized. While the NaH catalyzed reaction generates the cyclohexadiene enaminonitriles in high yields with heterocyclic substrates, the reaction fails to promote product formation of aliphatic alkyl substrates. On the contrary, the LDA mediated synthesis favors the long chain alkyl substituents while reactions involving the aromatic substrates result in low yields. The final conversion to the quinazolines is also a modification on literature protocols. In cellular assays, the quinazolines showed the most promising activity against Jurkat with CC(50) values in the low micromolar range. Weak activity was observed against microbial strains (Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae). The substituted enaminonitrile intermediates also exhibited weak anti-microbial activity and cytotoxicity against human T-cell leukemia.

New antibiotics from bacterial natural products

For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial sources. In particular, efforts have refocused on finding new antibiotics from old sources (for example, streptomycetes) and new sources (for example, other actinomycetes, cyanobacteria and uncultured bacteria). This has resulted in several newly discovered antibiotics with unique scaffolds and/or novel mechanisms of action, with the potential to form a basis for new antibiotic classes addressing bacterial targets that are currently underexploited.

Charting Biological and Chemical Space: PSSC and SCONP as Guiding Principles for the Development of Compound Collections Based on Natural Product Scaffolds.

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Charting Biological and Chemical Space: PSSC and SCONP as Guiding Principles for the Development of Compound Collections Based on Natural Product Scaffolds

AbstractFinding small molecules that selectively modulate protein function remains one of the major challenges in the fields of chemogenomics and drug development. Natural products interact with proteins in their biosynthesis and when displaying biological activity, and can therefore be considered as “privileged structures”. Thus, natural products may serve as biologically validated starting points for the design of focused compound collections. In recent years, effective synthesis methods for natural‐product‐based focused compound collections have been developed, including multi‐component reactions. This review discusses recent advances in the synthesis of natural‐product‐inspired compound collections as well as the application of Protein Structure Similarity Clustering (PSSC) and a Structural Classification Of Natural Products (SCONP) as guiding principles for the design of focused compound collections based on natural products.

Structure-Based Engineering of E. coli Galactokinase as a First Step toward In Vivo Glycorandomization

In vitro glycorandomization is a rapid chemoenzymatic strategy to diversify complex natural product scaffolds. The glycorandomization sugar activation pathway is dependent upon the efficient construction of diverse sugar-1-phosphate libraries. In the context of the previously evolved GalK Y371H "gatekeeper" mutation, the active site M173L mutation described herein presents a kinase with remarkably broadened substrate range to include 28 diverse natural and unnatural sugars. Among these new substrates, 6-azido-6-deoxy-galactose and 6-azido-6-deoxy-glucose present unique chemical probes to assess the utility of an E. coli Y371H/M173L-GalK-overproducing strain to generate unnatural sugar-1-phosphates in vivo. Remarkably, the in vivo conversion of both unnatural sugars rival that demonstrated in vitro. This notable in vivo success stands as the first step toward constructing short sugar-activation pathways in vivo and, ultimately, in vivo natural-product glycorandomization.

Design of compound libraries based on natural product scaffolds and protein structure similarity clustering (PSSC)

Recent advances in structural biology, bioinformatics and combinatorial chemistry have significantly impacted the discovery of small molecules that modulate protein functions. Natural products which have evolved to bind to proteins may serve as biologically validated starting points for the design of focused libraries that might provide protein ligands with enhanced quality and probability. The combined application of natural product derived scaffolds with a new approach that clusters proteins according to structural similarity of their ligand sensing cores provides a new principle for the design and synthesis of such libraries. This article discusses recent advances in the synthesis of natural product inspired compound collections and the application of protein structure similarity clustering for the development of such libraries.

Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery

Natural product analogs are significant sources for therapeutic agents. To capitalize efficiently on the effective features of naturally occurring substances, a natural product-based library production platform has been devised at Aurigene for drug lead discovery. This approach combines the attractive biological and physicochemical properties of natural product scaffolds, provided by eons of natural selection, with the chemical diversity available from parallel synthetic methods. Virtual property analysis, using computational methods described here, guides the selection of a set of natural product scaffolds that are both structurally diverse and likely to have favorable pharmacokinetic properties. The experimental characterization of several in vitro ADME properties of twenty of these scaffolds, and of a small set of designed congeners based upon one scaffold, is also described. These data confirm that most of the scaffolds and the designed library members have properties favorable to their utilization for creating libraries of lead-like molecules.

Enhancing marine natural product structural diversity and bioactivity through semisynthesis and biocatalysis.

In the last several decades the plants, animals and microbes from the marine environment have revealed a portion of what is clearly a tremendous resource for structurally diverse and bioactive secondary metabolites. Many of these extraordinarily sophisticated and bioactive natural products can be isolated in significant quantities without great difficulty. As a result these readily available bioactive natural products provide valuable starting materials for the rational generation of libraries of compounds prepared through semisynthesis and biocatalysis. A review of our work using marine natural products to generate rationally designed compound libraries and their biological activity against infectious diseases, cancer and neurological targets is presented. The marine natural products utilized to date as starting materials consist of compounds from a variety of structural classes and include: aureol, puupehenone, sarcophine, palinurin, and the manzamine alkaloids. The possibility to generate diverse bioactive products beginning with a marine natural product scaffold is a direct result of improvements made in the technologies to harvest samples from the ocean, purify and characterize complex natural products quickly and complete chemical reactions and biotransformations in parallel. As a result the vast resources of the ocean can now be utilized routinely to design and produce countless products to be evaluated as part of drug discovery and development programs.

Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering.

In vitro "glycorandomization" is a chemoenzymatic approach for generating diverse libraries of glycosylated biomolecules based on natural product scaffolds. This technology makes use of engineered variants of specific enzymes affecting metabolite glycosylation, particularly nucleotidylyltransferases and glycosyltransferases. To expand the repertoire of UDP/dTDP sugars readily available for glycorandomization, we now report a structure-based engineering approach to increase the diversity of alpha-d-hexopyranosyl phosphates accepted by Salmonella enterica LT2 alpha-d-glucopyranosyl phosphate thymidylyltransferase (E(p)). This article highlights the design rationale, determined substrate specificity, and structural elucidation of three "designed" mutations, illustrating both the success and unexpected outcomes from this type of approach. In addition, a single amino acid substitution in the substrate-binding pocket (L89T) was found to significantly increase the set of alpha-d-hexopyranosyl phosphates accepted by E(p) to include alpha-d-allo-, alpha-d-altro-, and alpha-d-talopyranosyl phosphate. In aggregate, our results provide valuable blueprints for altering nucleotidylyltransferase specificity by design, which is the first step toward in vitro glycorandomization.

Tandem Pummerer/Mannich cyclization cascade of alpha-sulfinylamides as a method to prepare aza-heterocycles.

A series of alpha-sulfinylenamides was conveniently prepared by the condensation of a primary amine with a ketone, followed by reaction of the resulting imine with ethylsulfenylacetyl chloride and subsequent oxidation with sodium periodate. When treated with p-TsOH, cyclization occurred to produce fused isoquinoline lactams by a mechanism that involves an initial Pummerer reaction followed by a subsequent cyclization of the resulting N-acyliminium ion onto the tethered aromatic ring. The isolation of a single diastereomer was rationalized in terms of a Nazarov-type 4pi-electrocyclic reaction followed by pi-cyclization onto the least hindered side of the N-acyliminium ion. Another method that was used to generate the alpha-acylthionium ion intermediate involved the reaction of bis(ethylsulfenylacetyl)acetamides with dimethyl(methyl)thiosulfonium tetrafluoroborate (DMTSF). Treatment of several bis-ethylsulfenylenamides with DMTSF delivered novel spiro-heterocycles as single diastereomers in good yield by a related process. The convergency and stereochemical control associated with this cascade sequence make it particularly suited for the assembly of natural product scaffolds. Some preliminary studies were directed toward both mesembrine and deethylibophyllidine. When the model Z-enamido sulfoxide 33 was heated with p-TsOH, a 80% yield of tosylate 34 was obtained as a single diastereomer. In this case, the carbocation intermediate derived from cyclization onto the terminal pi-bond was trapped with p-TsOH from the least hindered face, opposite the angular carbomethoxy and methyl groups. Related cyclization cascades were also found to occur with systems containing tethered indole rings.

Integrating natural product synthesis and combinatorial chemistry

The fields of natural product total synthesis and combinatorial chemistry have major differences as well as much in common. Unique to combinatorial chemistry is the need to devise rapid and efficient methods for parallel synthesis and purification, while an area of overlap is the targeting of natural product scaffolds for combinatorial libraries. Both these aspects are illustrated with examples from our research.