Synthesis of natural-product-based compound libraries

Advances in the discovery and development of anthelmintics by harnessing natural product scaffolds

Widespread resistance to currently-used anthelmintics represents a major obstacle to controlling parasitic nematodes of livestock animals. Given the reliance on anthelmintics in many control regimens, there is a need for the continued discovery and development of new nematocides. Enabling such a focus are: (i) the major chemical diversity of natural products; (ii) the availability of curated, drug-like extract-, fraction- and/or compound-libraries from natural sources; (iii) the utility and practicality of well-established whole-worm bioassays for Haemonchus contortus-an important parasitic nematodes of livestock-to screen natural product libraries; and (iv) the availability of advanced chromatographic (HPLC), spectroscopic (NMR) and spectrometric (MS) techniques for bioassay-guided fractionation and structural elucidation. This context provides a sound basis for the identification and characterisation of anthelmintic candidates from natural sources. This chapter provides a background on the importance and impact of helminth infections/diseases, parasite control and aspects of drug discovery, and reviews recent work focused on (i) screening well-defined compound libraries to establish the methods needed for large-scale screening of natural extract libraries; (ii) discovering plant and marine extracts with nematocidal or nematostatic activity, and purifying bioactive compounds and assessing their potential for further development; and (iii) synthesising analogues of selected purified natural compounds for the identification of possible 'lead' candidates. The chapter describes some lessons learned from this work and proposes future areas of focus for drug discovery. Collectively, the findings from this recent work show potential for selected natural product scaffolds as candidates for future development. Developing such candidates via future chemical optimisation, efficacy and safety evaluations, broad spectrum activity assessments, and target identification represents an exciting prospect and, if successful, could pave the way to subsequent pre-clinical and clinical evaluations.

The synthetic tubulysin derivative, tubugi-1, improves the innate immune response by macrophage polarization in addition to its direct cytotoxic effects in a murine melanoma model

Synthetic tubugis are equally potent but more stable than their natural forms. Their anticancer potential was estimated on a solid melanoma in vitro and in vivo. Tubugi-1 induced the apoptosis in B16 cells accompanied with strong intracellular production of reactive species, subsequently imposing glutathione and thiol group depletion. Paradoxically, membrane lipids were excluded from the cascade of intracellular oxidation, according to malondialdehyde decrease. Although morphologically apoptosis was typical, externalization of phosphatidylserine (PS) as an early apoptotic event was not detected. Even their exposition is pivotal for apoptotic cell eradication, primary macrophages successfully eliminated PS-deficient tubugi-1 induced apoptotic cells. The tumor volume in animals exposed to the drug in therapeutic mode was reduced in comparison to control as well as to paclitaxel-treated animals. Importantly, macrophages isolated from tubugi-1 treated animals possessed conserved phagocytic activity and were functionally and phenotypically recognized as M1. The cytotoxic effect of tubugi-1 is accomplished through its ability to polarize the macrophages toward M1, probably by PS independent apoptotic cell engulfment. The unique potential of tubugi-1 to prime the innate immune response through the induction of a specific pattern of tumor cell apoptosis can be of extraordinary importance from fundamental and applicable aspects.

Prediction of Medicinal Properties Using Mathematical Models and Computation, and Selection of Plant Materials

In any phytochemical drug discovery programme, one of the major issues is the appropriate selection of target plant species that may provide lead for new drug discovery and development. Conducting research without any working hypotheses may produce serendipitous discoveries, but the chances of success are much slimmer than any information-based targeted approach. Therefore, the plant selection process is extremely important for ensuring success. In recent years, there have been significant amounts of work involving applications of various mathematical modelling and computational techniques to predict medicinal properties of plants, and thus to provide information-based selection of plant materials for further studies aiming at potential drug discovery and development. This chapter presents an overview of methods and processes involved in plant selection by utilizing various mathematical modelling and computational techniques.

A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine

Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated.

An ortho C-methylation/O-glycosylation motif on a hydroxy-coumarin scaffold, selectively installed by biocatalysis

To achieve near quantitative dual modification of the hydroxy-coumarin scaffold, the C-methylation had to occur strictly before the O-glucosylation.

Modular, One-Pot, Sequential Aziridine Ring Opening-S(N)Ar Strategy to 7-, 10-, and 11-Membered Benzo-Fused Sultams

The generation of common and stereochemically rich medium-sized benzo-fused sultams via complementary pairing of heretofore-unknown (o-fluoroaryl)sulfonyl aziridine building blocks with an array of amino alcohols/amines in a modular one-pot, sequential protocol using an aziridine ring opening and intramolecular nucleophilic aromatic substitution is reported. The strategy employs a variety of amino alcohols/amines and proceeds with 6 + 4/6 + 5 and 6 + 1 cycloetherification pathways in a highly chemo- and regioselective fashion to obtain skeletally and structurally diverse, polycyclic, 10- to 11- and 7-membered benzo-fused sultams for broad-scale screening.

Synthesis of a natural product-like compound collection through oxidative cleavage and cyclization of linear peptides

Massive efforts in molecular library synthesis have strived for the development of synthesis methodology which systematically delivers natural product-like compounds of high spatial complexity. Herein, we present a conceptually simple approach that builds on the power of solid-phase peptide synthesis to assemble precursor peptides (oligomers) designed to undergo oxidative cascade reactions. By harnessing the structural side-chain diversity and inherent stereochemical features offered by readily available amino acids (monomers), a proof-of-concept collection of 54 skeletally and stereochemically diverse compounds was generated, and selected compounds were elaborated into isoform-selective metalloprotease inhibitors.

Regioselective polymethylation of α-(1 → 4)-linked mannopyranose oligosaccharides

An approach has been developed of the regioselective methylation of α-(1 → 4)-linked mannopyranose oligosaccharides via a four-step methodology. The key reaction involved n-Bu2SnCl2-mediated activation of cis-diols. By tuning protecting groups on the substrates, multiple cis-diols in the substrates were functionalized in a consistent and regioselective manner. Using optimized substrates and reaction conditions, regioselective methylation of di-, tri-, and tetrasaccharide substrates proceeded in isolated yields per cis-diol of 95, 88 and 79%, respectively. The methodology was also applied to functionalize trans-diols in α-cyclodextrin.

Facile synthesis of 4-substituted 3,4-dihydrocoumarins via an organocatalytic double decarboxylation process

3,4-Dihydrocoumarins, considered to be valuable building blocks, have attracted considerable attention due to their various biological activities. Herein, we have documented an efficient and convenient double decarboxylation process for the synthesis of 4-substituted 3,4-dihydrocoumarin in moderate to excellent yields under mild reaction conditions (up to 98%).

Microwave-assisted linear approach toward highly substituted benzo[d]oxazol-5-yl-1H-benzo[d]imidazole on ionic liquid support

A novel and efficient diversity-oriented synthetic approach was employed to access the benzo[d]oxazol-5-yl-1H-benzo[d]imidazole on ionic liquid support, which helps to absorb microwave irradiation. In this paper, we successfully coupled 4-hydroxy-3-nitrobenzoic acid onto ionic liquid-immobilized o-phenylenediamine, which subsequently underwent an acid mediated, ring closure reaction leading to benzimidazole derivatives. After hydrogenation of the nitro group to an amine, the resulting ionic liquid conjugate was reacted with 1,1-thiocarbonyldiimidazols to yield an ionic liquid tagged-benzoxazol. Final skeletal diversity of the present scaffold was further achieved by S-alkylation with alkyl and aryl bromides. The benzo[d]oxazol-5-yl-1H-benzo[d]imidazole was finally cleaved smoothly from the ionic liquid support with sodium methoxide in methanol under microwave irradiation. This methodology has provided access to a small, diverse library by straightforward and simple operations and could be applied readily in various drug discovery programs.

Follow-up of natural products isolation

Follow-up of natural products isolation refers to re-isolation of compound(s) of interest in larger amounts for further pharmacological testing, conclusive structure elucidation, structure modifications to synthesize analogs for structure-activity relationships (SAR) studies, preformulation and formulation studies or clinical trials. In addition to conventional synthetic chemistry approaches, several other methodologies can be applied for following-up natural products isolation. This chapter outlines, with specific examples, various strategies and methods involved in follow-up of natural products isolation.

Solid-phase parallel synthesis of a tetrahydroindazolone library containing three unique core skeletons

We have developed a practical strategy for the regioselective synthesis of a 1-(hetero)aryl-3-substituted tetrahydroindazolone library. The condensation of in situ generated arylhydrazine on solid supports with 2-acylcyclohexane-1,3-diones ensured the efficiency of solid-phase parallel synthesis. In addition, we introduced three unique core skeletons containing nitrophenyl, anilyl, and pyridyl groups to maximize the molecular diversity through a diverse display of polar surface area in 3D chemical space. A 162-membered drug-like tetrahydroindazolone library was constructed in an average purity of 92% without further purification.

Synthesis of natural product inspired compound collections

Natural products, their derivatives, and their analogues are among the most important sources for new drug candidates and tools for chemical biology and medicinal chemistry research. Therefore, there is a need for the development of efficient synthesis methods which give access to natural product derived and inspired compound collections. To meet this challenge, the requirements of multistep stereoselective syntheses, and the logic and methodology of natural product total synthesis need to be translated and adapted to the methods and formats for the synthesis of compound collections. Recent developments in the synthesis of natural product inspired compound collections having carbocyclic and heterocyclic scaffolds highlight the fact that this goal can be successfully attained. The progress made has paved the way for the integration of natural product inspired compound collections into medicinal chemistry and chemical biology research.

A concise and diversity-oriented approach to the synthesis of SAG derivatives

An efficient and rapid solution-phase combinatorial synthesis of the SAG library was developed. The salient features for this library synthesis is the application of carbothioamide-derived palladacycle-catalyzed Suzuki coupling reactions for the parallel synthesis of a series of pyridine-based biaryl aldehydes under aerobic conditions and a direct N-alkylation of carbamates using NaH as base in DMF in the presence of catalytic amount of water. The resultant library has been submitted to biological screening to evaluate their potential role in the regulation of Hedgehog pathway.

A review of high throughput technology for the screening of natural products

High throughput screening is commonly defined as automatic testing of potential drug candidates at a rate in excess of 10,000 compounds per week. The aim of high throughput drug discovery is to test large compound collections for potentially active compounds ('hits') in order to allow further development of compounds for pre-clinical testing ('leads'). High throughput technology has emerged over the last few years as an important tool for drug discovery and lead optimisation. In this approach, the molecular diversity and range of biological properties displayed by secondary metabolites constitutes a challenge to combinatorial strategies for natural products synthesis and derivatization. This article reviews the approach of High throughput technique for the screening of natural products for drug discovery.

Synthesis of functionalized quinolines via Ugi and Pd-catalyzed intramolecular arylation reactions

Two types of quinoline scaffolds were constructed in a combinatorial format via the Ugi four-component reaction (U-4CR) and Pd-catalyzed intramolecular arylation reaction. The scope of this two-step synthetic sequence was examined from commercially available and synthetically accessible starting materials.

Synthesis of Steroid−Biaryl Ether Hybrid Macrocycles with High Skeletal and Side Chain Variability by Multiple Multicomponent Macrocyclization Including Bifunctional Building Blocks

Utilizing the multiple multicomponent macrocyclization including bifunctional building blocks (MiB) strategy, a library of nonracemic, nonrepetitive peptoid-containing steroid-biaryl ether hybrid macrocycles was built. Up to 16 new bonds, including those of the macrocyclization, can be formed in one pot simultaneously while introducing varied elements of diversity. Functional diversity is generated primarily by choosing Ugi-reactive functional building blocks, bearing the respective recognition or catalytic motifs. These appear attached to the peptoid backbone of the macrocyclic cavity, similar to side chains of amino acids found in enzyme active sites. Likewise, skeletal diversity is based on the variation of defined bifunctional building blocks which allow the parallel formation of macrocyclic cavities that are highly diverse in shape and size and thus perspectively in function. This straightforward approach is suitable to generate multifunctional macrocycles for applications in catalysis, supramolecular, or biological chemistry.

Design, synthesis, and biological evaluation of a scaffold for iGluR ligands based on the structure of (−)-dysiherbaine

The design and synthesis of four 2,2-disubstituted dihydrobenzofurans that are structurally related to several glutamate-containing natural products, including (-)-dysiherbaine, is described. Biological evaluation of these analogs shows that one is a KA receptor antagonist and another is an NMDA receptor agonist.

Solid-Phase Parallel Synthesis of Natural Product-Like Diaza-Bridged Heterocycles through Pictet−Spengler Intramolecular Cyclization

A multistep, practical solid-phase strategy for the synthesis of natural product-like diaza-bridged heterocycles was developed. A key step in the library synthesis is tandem acidolytic cleavage with subsequent in situ iminium formation followed by the Pictet-Spengler intramolecular cyclization. The Pictet-Spengler-type intramolecular cyclization step was regioselective and diastereoselective to give final products as single diastereomers in exceptional yields and purities, which was confirmed by NMR structural study and LC/MS analysis. This approach is exemplified by the preparation of a 384-member library of 3,9-diazabicyclo[3.3.1]non-6-en-2-one skeletons, fused with indole and dihydroxybenzene and diversified at two bridging nitrogen atoms, using the solid-phase parallel synthetic methodology without further purification. In this pilot library, two diastereomerically enriched diaza-bridged core skeletons were modified by amide and urea bond formation on bridging nitrogen atoms, and this scheme exhibits the potential for expansion to obtain further diversification.