Ring closure methods in the synthesis of macrocyclic natural products

Synthesis of [2+2] Schiff base macrocycles by a solvent templating strategy and halogen bonding directed assembly

Schiff base imine condensations are a useful tool for macrocycle synthesis and applications within supramolecular chemistry. Here we address the mixtures of products that can arise from template free synthesis using dicarbonylheterocycles and diamines, and look to develop metal-free template methods for selective macrocycle formation. A range of alkyl α,ω-diamines were combined with phenanthroline and pyridine heterocyclic dicarbaldehydes under standard literature conditions. The reaction conditions were modified to demonstrate a relationship between choice of solvent and product equilibria. It was observed that benzene and toluene could shift a mixture of products and unreacted starting materials to form predominantly one imine product for a number of systems. Once the macrocyclic products had been characterized in selected solvents, iodinated halogen bonding guest molecules were added to direct macrocycle assemblies using non-covalent interactions. Studies to investigate host – guest suitability and halogen bond interactions were conducted, and it was found that tetraiodoethylene had an influence on the formation of a phenanthroline based macrocycle. Proof of concept experiments were performed to show the influence of the guest molecule, tetraiodoethylene, on the macrocyclic products formed under competitive dynamic combinatorial chemistry conditions.

4-(Dimethylamino)pyridine N-Oxide-Catalyzed Macrolactamization Using 2-Methyl-6-nitrobenzoic Anhydride in the Synthesis of the Depsipeptidic Analogue of FE399

A depsipeptidic analogue of FE399 was efficiently synthesized mainly through macrolactamization using 2-methyl-6-nitrobenzoic anhydride (MNBA), and a detailed investigation of the desired 16-membered macrolactam core of FE399 was performed. It was determined that the combination of MNBA and a catalytic amount of 4-(dimethylamino)pyridine N-oxide exhibits much higher activity than that of conventionally used coupling reagents such as hexafluorophosphate azabenzotriazole tetramethyl uronium and benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate.

Lactones in the Synthesis of Prostaglandins and Prostaglandin Analogs

In the total stereo-controlled synthesis of natural prostaglandins (PGs) and their structural analogs, a vast class of compounds and drugs, known as the lactones, are encountered in a few key steps to build the final molecule, as: δ-lactones, γ-lactones, and 1,9-, 1,11-, and 1,15-macrolactones. After the synthesis of 1,9-PGF2α and 1,15-PGF2α lactones, many 1,15-lactones of E2, E3, F2, F3, A2, and A3 were found in the marine mollusc Tethys fimbria and the quest for understanding their biological role stimulated the research on their synthesis. Then 1,9-, 1,11-, and 1,15-PG lactones of the drugs were synthesized as an alternative to the corresponding esters, and the first part of the paper describes the methods used for their synthesis. The efficient Corey procedure for the synthesis of prostaglandins uses the key δ-lactone and γ-lactone intermediates with three or four stereocenters on the cyclopentane fragment to link the PG side chains. The paper describes the most used procedures for the synthesis of the milestone δ-Corey-lactones and γ-Corey-lactones, their improvements, and some new promising methods, such as interesting, new stereo-controlled and catalyzed enantioselective reactions, and methods based on the chemical/enzymatic resolution of the compounds in different steps of the sequences. The many uses of δ-lactones not only for the synthesis of γ-lactones, but also for obtaining 9β-halogen-PGs and halogen-substituted cyclopentane intermediates, as synthons for new 9β-PG analogs and future applications, are also discussed.

Iterative Assembly of Macrocyclic Lactones using Successive Ring Expansion Reactions

Macrocyclic lactones can be prepared from lactams and hydroxyacid derivatives via an efficient 3- or 4-atom iterative ring expansion protocol. The products can also be expanded using amino acid-based linear fragments, meaning that macrocycles with precise sequences of hydroxy- and amino acids can be assembled in high yields by "growing" them from smaller rings, using a simple procedure in which high dilution is not required. The method should significantly expedite the practical synthesis of diverse nitrogen containing macrolide frameworks.

Lewis acid catalyzed intramolecular [3 + 2] cross cycloadditions of cobalt-alkynylcyclopropane 1,1-diesters with carbonyls for construction of medium-sized and polycyclic skeletons

A Lewis acid catalyzed intramolecular [3 + 2] cross cycloaddition of cobalt-alkynylcyclopropane 1,1-diesters with carbonyls has been successfully developed. Together with simple and efficient postcycloadditions of the cobalt-alkyne moiety, a general and efficient strategy for construction of structurally complex and diverse medium-sized skeletons and related polycycles was supplied successfully.

Discovery of the macrocycle 11-(2-pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene (SB1518), a potent Janus kinase 2/fms-like tyrosine kinase-3 (JAK2/FLT3) inhibitor for the treatment of myelofibrosis and lymphoma

Discovery of the activating mutation V617F in Janus Kinase 2 (JAK2(V617F)), a tyrosine kinase critically involved in receptor signaling, recently ignited interest in JAK2 inhibitor therapy as a treatment for myelofibrosis (MF). Herein, we describe the design and synthesis of a series of small molecule 4-aryl-2-aminopyrimidine macrocycles and their biological evaluation against the JAK family of kinase enzymes and FLT3. The most promising leads were assessed for their in vitro ADME properties culminating in the discovery of 21c, a potent JAK2 (IC(50) = 23 and 19 nM for JAK2(WT) and JAK2(V617F), respectively) and FLT3 (IC(50) = 22 nM) inhibitor with selectivity against JAK1 and JAK3 (IC(50) = 1280 and 520 nM, respectively). Further profiling of 21c in preclinical species and mouse xenograft and allograft models is described. Compound 21c (SB1518) was selected as a development candidate and progressed into clinical trials where it is currently in phase 2 for MF and lymphoma.

Synthesis of oligomeric 4-(glycosyloxy)benzoate macrocyclic glycosides

Clemoarmanoside A and Clemahexapetoside A, two novel cyclic dimers of 4-(glycosyloxy)benzoates containing the unusual d-allopyranose as one of the sugar units, were synthesized for the first time. The convenient synthetic approach was adapted to the assembly of the symmetrical trimeric, tetrameric, and pentameric congeners. The synthesis clarified the discrepancy in the NMR data reported for the natural products. X-ray diffraction analysis of Clemahexapetoside A revealed that it adopted an armchair conformation with two carbohydrate rings as the arms and two aromatic rings as the back and seat, respectively.

Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis

The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon-carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give beta-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products.

Natural macrocyclic molecules have a possible limited structural diversity

This paper examines ring size patterns of natural product macrocycles. Evidence is presented that natural macrocycles containing 14-, 16-, and 18-membered rings are of frequent occurrence based on a data mining study. The results raise a question about the limited diversity of macrocycle ring sizes and the nature of the constraints that may cause them. The data suggest that the preference bears no relationship to the odd-even frequency in natural fatty acids. The trends reported here, along with those reported previously (Wessjohann et al. (2005) Mol Divers 9:171), may be generalized to better understand the possible structure preferences of natural macrocycles.

Polyether macrocycles from intramolecular cyclopropanation and ylide formation. Effect of catalyst and coordination

The use of catalytic metal carbene methodology with diazoacetates for the construction in high yield of polyether macrocycles having ring sizes greater than 25 has been achieved by preventing access to gamma-C-H positions for intramolecular insertion. Cyclopropanation is the exclusive outcome of reactions performed with dirhodium(II) catalysts, and product yields of greater than 70% are obtained without resorting to high dilution with solvents. With copper(I) catalysts having multiple sites for polyether coordination, intramolecular oxonium ylide formation occurs at the terminal oxygen, followed by [2,3]-sigmatropic rearrangement of the pendant allyl group, in competition with cyclopropanation. Sodium ion coordination with the reactant diazo compound inhibits oxonium ylide formation in copper-catalyzed reactions. The composite results are consistent with copper serving as a template for the substrate as well as the site in the ether complex for diazo decomposition and subsequent metal carbene reactions.

Short and Efficient Approach Towards Macrocyclic Lactones Based on a Sonogashira Reaction

Polyketide-derived macrolactones like zearalenone (1), zearalane (2) or curvularin (3) display a wide range of interesting pharmacological activities. Here, we present a short and efficient approach towards this class of natural products by a combination of the Sonogashira and Mitsunobu reactions. The resulting lactone 9 was tested against human cancer cell lines at the NCI.

Highly efficient, one-step macrocyclizations assisted by the folding and preorganization of precursor oligomers

Highly efficient, one-step macrocyclizations leading to the formation of macrocyclic hexa(aramides) in high yields (69-82%) are described. The one-step macrocyclizations were facilitated by the preorganization or folding of the backbones of uncyclized precursors in the course of macrocyclization. The preorganization of backbones was achieved by the presence of localized three-centered hydrogen bonds that were adopted in the design of a class of closely related, backbone-rigidified foldamers. The macrocyclization involved reactions between diacid chloride 1 and diamine 2. The crude reaction mixtures and products were conveniently examined by mass spectrometric method (MALDI-TOF). Compared to most traditional one-step macrocyclizations that usually require high dilution conditions and often lead to very low overall yields of the desired products, cyclic hexamers 3 were obtained as the overwhelmingly major product under a variety of reaction conditions, suggesting the generality of this approach.

Synthetic Studies Aimed at (−)-Cochleamycin A. Evaluation of Late-Stage Macrocyclization Alternatives

An efficient route to the fully functionalized ABC ring systems of the unnatural enantiomer of cochleamycin A was developed. L-(-)-Malic and L-(-)-ascorbic acids served well as starting materials for the two building blocks used to construct an (E,Z,E)-1,6,8-nonatriene intermediate. The AB part structure was assembled by way of a stereocontrolled intramolecular Diels-Alder cycloaddition via adoption of an endo transition state. From this vantage point, two general pathways were subsequently explored as to their suitability for elaboration of the CD rings. Initially examined was a protocol involving 10-membered carbocycle construction. When this approach was demonstrated not to be workable, attention was directed to 10-membered macrolactonization as an alternative tactic. Although assembly of the C-ring in this manner was easily achieved, ultimate closure of the six-membered ring to form ring D remains an unsolved problem.

Total Synthesis of Formamicin

The enantioselective total synthesis of the cytotoxic plecomacrolide natural product formamicin (1) is described. Key aspects of this synthesis include the efficient transacetalation reactions of MOM ethers 28 and 38 to form the seven-membered formyl acetals 29 and 39, a late-stage Suzuki cross-coupling reaction of the highly functionalized vinyl boronic acid 6 and vinyl iodide 7, a highly beta-selective glycosidation reaction of beta-hydroxy ketone 4 with 2,6-dideoxy-2-iodoglucopyranosyl fluoride 3, and the global desilylation of penultimate intermediate 77 mediated by in situ generated Et(3)N.2HF.

Total synthesis of the formamicin aglycon, formamicinone

[structure: see text] The total synthesis of formamicinone (2), the aglycone of formamicin (1), has been accomplished via the late-stage Suzuki cross-coupling of fragments 5 and 6, the macrolactonization of seco ester 14, and the Mukaiyama aldol reaction of aldehyde 3 and methyl ketone 4. An efficient and highly stereoselective second generation synthesis of vinyl iodide 6 is also described.

Total synthesis of (-)-bafilomycin A(1)

A highly stereoselective total synthesis of (-)-bafilomycin A(1), the naturally occurring enantiomer of this potent vacuolar ATPase inhibitor, is described. The synthesis features the highly stereoselective aldol reaction of methyl ketone 8b and aldehyde 60c and a Suzuki cross-coupling reaction of the highly functionalized advanced intermediates 12 and 39. Vinyl iodide 12 was synthesized by a 14-step sequence starting from the readily available beta-alkoxy aldehyde 14, while the vinylboronic acid component 39 was synthesized by a nine-step sequence from beta-hydroxy-alpha-methyl butyrate 44 via a sequence involving the alpha-methoxypropargylation of chiral aldehyde 49 with the alpha-methoxypropargylstannane reagent 54. Syntheses of fragments 12 and 39 also feature diastereoselective double asymmetric crotylboration reactions to set several of the critical stereocenters. The Suzuki cross-coupling of 12 and 39 provided seco ester 40, which following conversion to the seco acid underwent smooth macrolactonization to give 41. The success of the macrocyclization required that C(7)-OH be unprotected. The Mukaiyama aldol reaction between aldehyde 60c and the TMS enol ether generated from 8b provided aldol 65 with high diastereoselectivity. Finally, all silicon protecting groups were removed by treatment of the penultimate intermediate 65 with TAS-F (tris(dimethylamino)sulfonium difluorotrimethylsilicate), thereby completing the total synthesis of (-)-bafilomycin A(1).

Studies on the synthesis of (-)-spinosyn a: application of the steric directing group strategy to transannular Diels-Alder reactions

A highly diastereoselective and enantioselective synthesis of the decahydro-as-indacene nucleus 12 of (-)-spinosyn A (1) is reported. By implementing the steric directing group strategy, tricyclic lactone 37 was produced from a remarkably diastereoselective transannular Diels-Alder reaction of lactone 9. The tricyclic core of the natural product was then obtained by using an Ireland-Claisen ring contraction of 37. Reversal of the order of these two steps resulted in an almost complete loss of diastereoselectivity.

Studies on the synthesis of the decahydro-as-indacene ring system of (-)-spinosyn A via transannular Diels-Alder reactions of substituted (E,E,E)-cyclododeca-1,6,8-trienes

Stereoselective syntheses of decahydro-as-indacenes 31 and 54 are reported. The key features of our syntheses of 31 and 54 are the tandem Ireland-Claisen ring contraction of lactones 29 and 38 followed by the transannular Diels-Alder cyclization of cyclododecatrienes 30 and 35. Transition state modeling of both the transannular Diels-Alder reaction and the Ireland-Claisen ring contraction using PCModel is also described.Key words: transannular Diels-Alder reactions, tandem reactions, Claisen ring contraction, Spinosyn A, synthetic study.

Total synthesis and conformational studies of hapalosin, N-desmethylhapalosin and 8-deoxyhapalosin

Hapalosin (2), a 12-membered cyclic depsipeptide possessing MDR-reversing activity, and analogues (3) and (4) have been synthesized using macrolactamization as an important ring-forming step. Three building blocks: (2S,3R)-3-(tert-butyldimethylsilyloxy)-2-methyl-decanoic acid (13), benzyl (S)-2-hydroxy-3-methylbutanate (14), and (4S,3R)-4-(benzyloxycarbonyl-methylamino)-3-methoxymethoxy-5-pheny l-pentanoic acid (28) were prepared from Evans's chiral imide (9), L-valine, and L-N-Boc phenylalanine (17), respectively, and were assembled together by applying twice Yamaguchi's coupling methodology. A new and efficient selective N-methylation of gamma-hydroxy-beta-amino ester taking advantage of the vicinal amino alcohol function was uncovered in the course of this study. Thus, treatment of compound 19 with HCHO in the presence of catalytic amount of pTsOH followed by reduction (NaBH3CN, TFA, CH2Cl2) of the so-formed oxazolidine 24 gave the N-methylated product 25. Furthermore, a dual role of oxazolidine as protecting group of vicinal amino alcohol and latent N-methyl function was established which allowed synthesizing both hapalosin (2) and N-desmethylhapalosin (3) from the same linear precursor 32 in a step-efficient and atom economic way. In contrast to hapalosin (2) and N-desmethyl analogue (3), the amide bond of 8-deoxy hapalosin (4) exists at room temperature (CDCl3) exclusively in s-cis conformation as evidenced by NOE studies. This observation has been explained on the basis of computational studies. No significant MDR reversing activity of 8-deoxy hapalosin (4) was observed in K562 R and S/Adriblastine against human erythroleucemic cell lines indicating thus the important contribution of hydroxy group to the bioactivity of hapalosin.