Total Synthesis of a 28-Member Stereoisomer Library of Murisolins

Relative stereochemical determination of the C61-C83 fragment of symbiodinolide using a stereodivergent synthetic approach

Structural determination is required in the use of marine natural products to create novel drugs and drug leads in medicinal chemistry. Symbiodinolide, which is a polyol marine natural product with a molecular weight of 2860, increases the intracellular Ca2+ concentration and exhibits inhibitory activity against cyclooxygenase-1. Seventy percent of the structure of symbiodinolide has been stereochemically clarified. Herein, we report the elucidation of the relative configuration of the C61-C83 fragment, which is among the remaining thirty percent, using a stereodivergent synthetic strategy. We first assigned the relative configuration of the C61-C74 fragment. Two candidate diastereomers of the C61-C74 fragment were synthesized, and their NMR data were compared with those of the natural product, revealing the relative stereochemistry of this component. We then narrowed down the candidate compounds for the C69-C83 fragment from 16 possible diastereomers by analyzing the NMR data of the natural product, and we thus selected eight candidate diastereomers. Stereodivergent synthesis of the candidates for this fragment and comparison of the NMR data of the natural product and the eight synthetic products resulted in the relative stereostructural clarification of the C69-C83 fragment. These individually determined relative stereochemistries of the C61-C74 and C69-C83 fragments were connected via the common C69-C73 tetrahydropyran moiety of the fragments. Finally, the relative configuration of the C61-C83 fragment of symbiodinolide was determined. The stereodivergent synthetic approach used in this study can be extended to the stereochemical determination of other fragments of symbiodinolide.

Library construction of stereochemically diverse isomers of spirooliganin: their total synthesis and antiviral activity

The construction of libraries of stereoisomers of natural products serves as an important approach to investigating the correlation between the stereostructure and biological activity. However, the total synthesis and isomerzation of polycyclic scaffolds with multiple chrial centers are rare. Spirooliganin (1), a new skeleton natural product isolated from the plant Illicium oligandrum, was structurally characterized by comprehensive analysis of NMR spectroscopic data and ECD which revealed an unprecedented 5-6-6-6-7 polycyclic framework with six chiral centers. Here we report a 17-step total synthesis to prepare a library of stereochemically diverse isomers of spirooliganin, including 16 diastereoisomers and 16 regioisomers. In addition to a regioselective hetero-Diels-Alder cycloaddition, the synthetic strategy involves a photo-induced stereoselective Diels-Alder reaction, which gives only the abnormal trans-fused product as rationalized by density functional theory calculations. Preliminary biological evaluation showed that spirooliganin and regioisomers 39 exhibited potent inhibition of Coxsackievirus B3. It also revealed the pharmacophore effect of the D-ring (16R,18R,24R, and 26R) for their antiviral activities.

Asymmetric solution-phase mixture aldol reaction using oligomeric ethylene glycol tagged chiral oxazolidinones

Sorting tags are oligomeric structures that can be used as protecting groups or chiral auxiliaries enabling solution-phase mixture syntheses of multiple tagged compounds in one pot and allowing for facile and predictable chromatographic separation of products at the end of synthetic sequences. Perfluorinated hydrocarbon and oligomeric ethylene glycol (OEG) derivatives are known classes of sorting tags. Herein we describe the preparation of OEGylated chiral oxazolidinones and their use in asymmetric solution-phase mixture aldol reactions. Through the use of such oxazolidinones based on tyrosine four different individually tagged aldol adducts were obtained as a mixture, chromatographically demixed, detagged, and it was shown that these processes gave the desired aldol products in good yield and enantioselectivity.

Construction of Iterative Tetrahydrofuran Ring Units and Total Synthesis of (+)-Goniocin

Cytotoxic acetogenin (+)-goniocin has been synthesized in 17 steps from (R)-O-tritylglycidol. The core structure of the contiguous C22-C10 threo-trans-threo-trans-threo-trans-tris-tetrahydrofuran (THF) ring involving an iterative THF-ring unit was synthesized. An iterative THF ring unit was constructed from an alkenyl-substituted THF ring in four steps including a Pd(II)-catalyzed ring-closing reaction and cross-metathesis. This method is general and allows the preparation of both trans-threo-trans- and trans-threo-cis-THF ring units flexibly.

Catalytic Enantioselective Peroxidation of α,β-Unsaturated Aldehydes for the Asymmetric Synthesis of Biologically Important Chiral Endoperoxides

We have developed an unprecedented highly enantioselective catalytic peroxidation of enals. Critical to this development is the discovery that varying the structure of the hydroperoxide has a significant impact on the enantioselectivity of the organocatalytic asymmetric peroxidation. This novel transformation enabled the development of an enantioselective route toward the core structure shared by all members of the stolonoxide family of anticancer natural products, a connected trans-3,6-disubstituted-1,2-dioxane and trans-2,5-disubstituted-tetrahydrofuran ring system. Our route also features an unprecedented cyclization cascade of a chiral bis(epoxy)hydroperoxide. The new methodology and synthetic strategy established in this work should be applicable to the enantioselective synthesis of a broad range of chiral 1,2-dioxolanes and 1,2-dioxanes, thereby facilitating biological and medicinal chemistry studies of peroxy natural products.

Total synthesis, stereochemical assignment, and biological activity of chamuvarinin and structural analogues

A highly stereocontrolled synthesis of (+)-chamuvarinin has been completed in 1.5% overall yield over 20 steps. The key fragment coupling reactions were the addition of alkyne 8 to aldehyde 7 (under Felkin-Anh control), followed by the two step activation/cyclization to close the C20-C23 2,5-cis-substituted tetrahydrofuran ring and a Julia-Kocienski olefination at C8-C9 to introduce the terminal butenolide. The inherent flexibility of our coupling strategy led to a streamlined synthesis with 17 steps in the longest sequence (2.2% overall yield), in which the key bond couplings are reversed. In addition, a series of structural analogues of chamuvarinin have been prepared and screened for activity against HeLa cancer cell lines and both the bloodstream and insect forms of Trypanosoma brucei, the parasitic agent responsible for African sleeping sickness.

Concise synthesis and biological assessment of (+)-neopeltolide and a 16-member stereoisomer library of 8,9-dehydroneopeltolide: identification of pharmacophoric elements

We describe herein a concise synthesis of (+)-neopeltolide, a marine macrolide natural product that elicits a highly potent antiproliferative activity against several human cancer cell lines. Our synthesis exploited the powerful bond-forming ability and high functional group compatibility of olefin metathesis and esterification reactions to minimize manipulations of oxygen functionalities and to maximize synthetic convergency. Our findings include a chemoselective olefin cross-metathesis reaction directed by H-bonding, and a ring-closing metathesis conducted under non-high dilution conditions. Moreover, we developed a 16-member stereoisomer library of 8,9-dehydroneopeltolide to systematically explore the stereostructure-activity relationships. Assessment of the antiproliferative activity of the stereoisomers against A549 human lung adenocarcinoma, MCF-7 human breast adenocarcinoma, HT-1080 human fibrosarcoma, and P388 murine leukemia cell lines has revealed marked differences in potency between the stereoisomers. This study provides comprehensive insights into the structure-activity relationship of this important antiproliferative agent, leading to the identification of the pharmacophoric structural elements and the development of truncated analogues with nanomolar potency.

An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries

Integration of flexible data-analysis tools with cheminformatics methods is a prerequisite for successful identification and validation of "hits" in high-throughput screening (HTS) campaigns. We have designed, developed, and implemented a suite of robust yet flexible cheminformatics tools to support HTS activities at the Broad Institute, three of which are described herein. The "hit-calling" tool allows a researcher to set a hit threshold that can be varied during downstream analysis. The results from the hit-calling exercise are reported to a database for record keeping and further data analysis. The "cherry-picking" tool enables creation of an optimized list of hits for confirmatory and follow-up assays from an HTS hit list. This tool allows filtering by computed chemical property and by substructure. In addition, similarity searches can be performed on hits of interest and sets of related compounds can be selected. The third tool, an "S/SAR viewer," has been designed specifically for the Broad Institute's diversity-oriented synthesis (DOS) collection. The compounds in this collection are rich in chiral centers and the full complement of all possible stereoisomers of a given compound are present in the collection. The S/SAR viewer allows rapid identification of both structure/activity relationships and stereo-structure/activity relationships present in HTS data from the DOS collection. Together, these tools enable the prioritization and analysis of hits from diverse compound collections, and enable informed decisions for follow-up biology and chemistry efforts.

Bare-minimum fluorous mixture synthesis of a stereoisomer library of 4,8,12-trimethylnonadecanols and predictions of NMR spectra of saturated oligoisoprenoid stereoisomers

All four diastereomers of a typical saturated oligoisoprenoid, 4,8,12-trimethylnonadecanol, are made by an iterative three-step cycle with the aid of traceless thionocarbonate fluorous tags to encode configurations. The tags have a minimum number of total fluorine atoms, starting at zero and increasing in increments of one. With suitable acquisition and data processing, each diastereomer exhibits characteristic chemical shifts of methyl resonances in its (1)H and (13)C NMR spectra. Together, these shifts provide a basis to predict the appearance of the methyl region of the spectrum of every stereoisomer of higher saturated oligoisoprenoids.

Parallel chemistry in the 21st century

The tool chest of techniques, methodologies, and equipment for conducting parallel chemistry is larger than ever before. Improvements in the laboratory and developments in computational chemistry have enabled compound library design at the desks of medicinal chemists. This unit includes a brief background in combinatorial/parallel synthesis chemistry, along with a discussion of evolving technologies for both solid- and solution-phase chemistry. In addition, there are discussions on designing compound libraries, acquisition/procurement of compounds and/or reagents, the chemistry and equipment used for chemical production, purification, sample handling, and data analysis.

Transannular O-heterocyclization: a useful tool for the total synthesis of Murisolin and 16,19-cis-Murisolin

Transannular O-heterocyclization is applied as a key step in a total synthesis. This highly stereoselective and metal-free transformation introduces four stereocenters in one step. It was chosen to be the pivotal step in the synthesis of Murisolin and 16,19-cis-Murisolin, two annonaceous acetogenins. The efficiency of this synthesis is further illustrated by a stereodivergent late-stage separation of both synthetic routes.

Synthesis and profiling of a diverse collection of azetidine-based scaffolds for the development of CNS-focused lead-like libraries

The synthesis and diversification of a densely functionalized azetidine ring system to gain access to a wide variety of fused, bridged, and spirocyclic ring systems is described. The in vitro physicochemical and pharmacokinetic properties of representative library members are measured in order to evaluate the use of these scaffolds for the generation of lead-like molecules to be used in targeting the central nervous system. The solid-phase synthesis of a 1976-membered library of spirocyclic azetidines is also described.

Accessing Stereochemically Rich Sultams via Microwave-Assisted, Continuous Flow Organic Synthesis (MACOS) Scale-out

The generation of stereochemically-rich benzothiaoxazepine-1,1'-dioxides for enrichment of high-throughput screening collections is reported. Utilizing a microwave-assisted, continuous flow organic synthesis platform (MACOS), scale-out of core benzothiaoxazepine-1,1'-dioxide scaffolds has been achieved on multi-gram scale using an epoxide opening/S(N)Ar cyclization protocol. Diversification of these sultam scaffolds was attained via a microwave-assisted intermolecular S(N)Ar reaction with a variety of amines. Overall, a facile, 2-step protocol generated a collection of benzothiaoxazepine-1,1'-dioxides possessing stereochemical complexity in rapid fashion, where all 8 stereoisomers were accessed from commercially available starting materials.

Binary fluorous tagging enables the synthesis and separation of a 16-stereoisomer library of macrosphelides

Fluorous mixture synthesis minimizes the effort to synthesize small-molecule libraries by labelling the molecules rather than the reaction vessels. Reactants are labelled with fluorinated tags and products can later be demixed based on the fluorine content. A limit in the number of available tags can be overcome by using binary encoding so that a total of four tags can label uniquely a library of 16 compounds. This strategy, however, means that separation based on fluorine content alone is not possible. Here, we solve this problem by selectively removing one tag after an initial demixing step; a second demixing provides each individual compound. The usefulness of this strategy is demonstrated by the synthesis of a library that contains all 16 diastereomers of the natural products macrosphelides A and E. Macrosphelide D was not in this library, and so its assigned structure was incorrect. We determined its constitution by using NMR spectroscopy and its configuration by synthesizing four candidate stereoisomers.

Diversity-oriented synthesis of 13- to 18-membered macrolactams via ring-closing metathesis

An efficient build/couple/pair approach to diversity-oriented synthesis was employed to access several structurally complex macrolactams. In this paper, we describe the successful evaluation of ring-closing metathesis toward the systematic generation of skeletal diversity. By appropriately varying the nature and chain length of the alkenol fragment, a diverse collection of 13- to 18-membered macrolactams were obtained.

Catalytic diastereoselective petasis reactions

Multicomponent Petasis reactions: the first diastereoselective Petasis reaction catalyzed by chiral biphenols that enables the synthesis of syn and anti β-amino alcohols in pure form has been developed. The reaction exploits a multicomponent approach that involves boronates, α-hydroxy aldehydes, and amines.

1,3-allylic strain as a strategic diversification element for constructing libraries of substituted 2-arylpiperidines

Flipping diversity

Minimization of 1,3-allylic strain is a recurring element in the design of a stereochemically- and spatially-diverse collection of 2-arylpiperidines. Here, stereochemically-diverse scaffolding is first constructed using A1,3 strain to guide the regioselective addition of nucleophiles, which serve as handles for further substitution. N -substitution with alkyl and acyl substituents again leverages A1,3 strain to direct each stereoisomer to two different conformer populations, doubling the number of library members.

Synthesis and stereochemical assignment of (+)-chamuvarinin

A stereocontrolled total synthesis of (+)-chamuvarinin, isolated from the root extract of Uvaria Chamae, utilizes a convergent modular strategy to construct the adjacently linked C15−C28 ether array, followed by a late-stage Julia−Kocienski olefination to append the butenolide motif. This constitutes the first total synthesis of (+)-chamuvarinin, defining the relative and absolute configuration of this unique annonaceous acetogenin.

A minimalist NMR approach for the structural revision of mucoxin

In an attempt to revise the structural assignment of mucoxin, and faced with 64 diastereomeric possibilities, we resorted to the synthesis of truncated structures that contained the core stereochemical sites. Twelve stereochemical analogues were synthesized, their (1)H and (13)C NMR spectra were analyzed and four recurring stereochemical trends were distilled from the data. Applying the observed trends to the diastereomeric population pared the possible choices for the correct structure of mucoxin from 64 to 4. Synthesis of these analogues led to the identification of the correct structure of mucoxin.

An aldol-based build/couple/pair strategy for the synthesis of medium- and large-sized rings: discovery of macrocyclic histone deacetylase inhibitors

An aldol-based build/couple/pair (B/C/P) strategy was applied to generate a collection of stereochemically and skeletally diverse small molecules. In the build phase, a series of asymmetric syn- and anti-aldol reactions were performed to produce four stereoisomers of a Boc-protected γ-amino acid. In addition, both stereoisomers of O-PMB-protected alaninol were generated to provide a chiral amine coupling partner. In the couple step, eight stereoisomeric amides were synthesized by coupling the chiral acid and amine building blocks. The amides were subsequently reduced to generate the corresponding secondary amines. In the pair phase, three different reactions were employed to enable intramolecular ring-forming processes: nucleophilic aromatic substitution (S(N)Ar), Huisgen [3+2] cycloaddition, and ring-closing metathesis (RCM). Despite some stereochemical dependencies, the ring-forming reactions were optimized to proceed with good to excellent yields, providing a variety of skeletons ranging in size from 8- to 14-membered rings. Scaffolds resulting from the RCM pairing reaction were diversified on the solid phase to yield a 14 400-membered library of macrolactams. Screening of this library led to the discovery of a novel class of histone deacetylase inhibitors, which display mixed enzyme inhibition, and led to increased levels of acetylation in a primary mouse neuron culture. The development of stereo-structure/activity relationships was made possible by screening all 16 stereoisomers of the macrolactams produced through the aldol-based B/C/P strategy.

A "shortcut" Mosher ester method to assign configurations of stereocenters in nearly symmetric environments. Fluorous mixture synthesis and structure assignment of petrocortyne A

A "shortcut" of the advanced Mosher rule for use in assigning stereocenters in molecules with elements of local symmetry is proposed. A single Mosher ester is made, and the chemical shifts of pairs of resonances related by local symmetry are subtracted from each other (rather than from analogous resonances in the isomeric Mosher ester) to provide the configuration. Fluorous mixture synthesis is used to make a stereoisomer library of the four isomers of petrocortyne A. These samples and the derived Mosher esters are used to assign the (3S,14S) configuration to petrocortyne A and to validate both the standard and shortcut Mosher methods for use in the petrocortyne family of dialkynyl carbinols.

Synthesis of a 35-member stereoisomer library of bistramide A: evaluation of effects on actin state, cell cycle and tumor cell growth

Synthesis and preliminary biological evaluation of a 35-member library of bistramide A stereoisomers are reported. All eight stereoisomers of the C1-C13 tetrahydropyran fragment of the molecule were prepared utilizing crotylsilane reagents 9 and 10 in our [4+2]-annulation methodology. In addition, the four isomers of the C14-C18 gamma-amino acid unit were accessed via a Lewis acid mediated crotylation reaction with use of both enantiomers of organosilane 11. The spiroketal subunit of bistramide A was modified at the C39-alcohol to give another point of stereochemical diversification. The fragments were coupled by using a standard peptide coupling protocol to provide 35 stereoisomers of the natural product. These stereochemical analogues were screened for their effects on cellular actin and cytotoxicity against cancer cell lines (UO-31 renal and SF-295 CNS). The results of these assays identified one analogue, 1.21, with enhanced potency relative to the natural product, bistramide A.

Assignment of the structure of petrocortyne A by mixture syntheses of four candidate stereoisomers

Two different mixture synthesis routes have been used to make the four stereoisomers of petrocortyne A. A first quick and dirty route provided a mixture of the four isomers in nonselective fashion. Mosher and 2-naphthylmethoxyacetic acid (NMA) ester methods were developed to identify the components, and the mixture was partially resolved on analytical chiral HPLC to give the two pure enantiomers of petrocortyne A and the racemate of its diastereomer. A second fluorous mixture synthesis produced all four isomers of petrocortyne A in individual pure form. Comparison of spectra of Mosher derivatives of the synthetic isomers with two supposedly different natural products showed that both natural samples were instead identical and had the (3S,14S) configuration. Likewise, petrocortynes B, D, and F-H are (3S,14S) and petrocortyne D is (3R,14S). Having access to all possible candidate isomers of both petrocortyne A and its Mosher derivatives provided a secure structure assignment not so much because one of the isomers matched the natural product, but because all of the other isomers did not.

Making mixtures to solve structures: structural elucidation via combinatorial synthesis

A domino Horner-Wadsworth-Emmons olefination strategy has been used to prepare homologous series of (polyen)ones, and through combinatorial elaboration, corresponding families of highly branched hydrocarbons. Gas chromatography-mass spectrometry of the mixtures has enabled the rapid and unambiguous identification of several highly branched alkanes of geochemical importance. This is the first example of the use of combinatorial synthesis for the elucidation of structural connectivity.

Comparison of the Relative Reactivities of the Triisopropylsilyl Group With Two Fluorous Analogs

The relative stabilities of two fluorous analogs, diisopropyl(3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluorodecyl)silyl and diisopropyl-(4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,11-heptadeca-fluoroundecyl)silyl [C(8)F(17)(CH(2))(n)Si(i-Pr)(2), where n = 2 or 3], of the standard triisopropylsilyl (TIPS) group are compared in the setting of alcohol protection. The fluorous silyl groups can be installed under standard conditions in comparable yields to the TIPS group, but the derived fluorous silyl ethers are more labile than TIPS ethers towards cleavage by both acids and fluoride.

Alteration of the bis-tetrahydrofuran core stereochemistries in asimicin can affect the cytotoxicity

A systematic analysis using 10 synthetic asimicin stereoisomers revealed that the stereochemistry of the bis-tetrahydrofuran core, including the tetrahydrofuran rings and the adjacent hydroxy functions, had significant effect on its cytotoxicity. Our findings set to rest the highly controversial perception that the stereochemistry of the tetrahydrofuran core has little effect on the activity, which is not true for its cytotoxic effect, and also reinforces the previous conclusion that asimicin is a highly potent anticancer compound.

Recent progress on the total synthesis of acetogenins from Annonaceae

An overview of recent progress on the total synthesis of acetogenins from Annonaceae during the past 12 years is provided. These include mono-tetrahydrofurans, adjacent bis-tetrahydrofurans, nonadjacent bis-tetrahydrofurans, tri-tetrahydrofurans, adjacent tetrahydrofuran-tetrahydropyrans, nonadjacent tetrahydrofuran-tetrahydropyrans, mono-tetrahydropyrans, and acetogenins containing only gamma-lactone. This review emphasizes only the first total synthesis of molecules of contemporary interest and syntheses that have helped to correct structures. In addition, some significant results on the novel synthesis and structure-activity relationship studies of annonaceous acetogenins are also introduced.

Tuning the acyclic ether moiety of anticancer agent AA005 with conformationally constrained fragments

A new series of anticancer annonaceous acetogenin mimetics were designed, synthesized, and evaluated based on our previously developed compound AA005, in which a variety of conformationally constrained fragments were introduced. Parallel syntheses of all new compounds were accomplished by replacement of the acyclic bis-ether functionality of AA005 with certain conformationally constrained fragments. Slight effects to the anticancer activity were exerted by altering stereochemistries in the middle modification region. Similar to AA005, most newly synthesized mimetics were found to exhibit potent activities against breast cancer cells, and showed satisfactory selectivities between cancerous and non-cancerous cells. An N,N'-dimethyl bis-amide compound 67 exhibits 30 times more potency against MDA-MB-468 cells than its parent molecule AA005. This study indicates that the introduction of appropriate conformational constraints is a useful optimizing tool for this class of anticancer agents. Successes in the bis-amide analogues of AA005 make this unique class of anticancer agents much simpler and more flexible for future further developments.