Bicyclic Scaffold Research Articles

Skeletal diversification by C-C cleavage to access bicyclic frameworks from a common tricyclooctane intermediate.

Herein, the diversification of tricyclo[3.2.1.03,6]octane scaffolds to afford diverse bicyclic scaffolds is described. The strained tricyclooctanes are prepared in two steps featuring a blue light-mediated [2+2] cycloaddition. Strategies for the cleavage of this scaffold were then explored resulting in the selective syntheses of the bicyclo[3.1.1]heptane, bicyclo[3.2.1]octane, and bicyclo[3.2.0]heptane cores. These findings may guide future studies of C-C cleavage reactions in strained carbon frameworks and their application in complex molecule synthesis.

Norbornene and Related Structures as Scaffolds in the Search for New Cancer Treatments.

The norbornene scaffold has arisen as a promising structure in medicinal chemistry due to its possible therapeutic application in cancer treatment. The development of norbornene-based derivatives as potential chemotherapeutic agents is attracting significant attention. Here, we report an unprecedented review on the recent advances of investigations into the antitumoral efficacy of different compounds, including the abovementioned bicyclic scaffold in their structure, in combination with chemotherapeutic agents or forming metal complexes. The impact that structural modifications to these bicyclic compounds have on the antitumoral properties and the mechanisms by which these norbornene derivatives act are discussed in this review. In addition, the use of norbornene, and its related compounds, encapsulation in nanosystems for its use in cancer therapies is here detailed.

An Enantioselective Approach to Heteroatom‐Containing Bicyclic Derivatives via Inverse‐Electron‐Demand Diels−Alder Reactions

Comprehensive SummaryChiral heteroatom‐containing bicyclic scaffolds are important pharmacophores and prevalent in bioactive natural products and drug molecules. Herein, we report a unified approach for the divergent synthesis of chiral heteroatom‐containing bicyclic derivatives by lanthanide (III)‐catalyzed asymmetric inverse‐electron‐demand Diels–Alder reactions of 2‐pyrones. These reactions occur with various readily available dihydropyrroles and dihydrofurans as dienophiles, providing a step‐economical synthetic platform for densely functionalized cis‐hydroindoles and cis‐hydrobenzofurans with excellent yields and enantioselectivities. The synthetic utility of this approach is demonstrated by the concise synthesis of (–)‐α‐lycorane and (–)‐lycorine alkaloids.

Synthesis of Polysubstituted 2-Oxabicyclo[2.1.1]hexanes via Visible-Light-Induced Energy Transfer.

Synthesis of bicyclic scaffolds has attracted growing interest because they are of high importance in modern pharmaceutical development. Here we report a strategy to access polysubstituted 2-oxabicyclo[2.1.1]hexanes in a single operation from readily accessible benzoylformate esters and bicyclo[1.1.0]butanes via visible-light-induced triplet energy transfer catalysis. The process is proposed to involve a formal [2π + 2σ] photocycloaddition/backbone C-H abstraction/aryl group migration sequence. A diverse range of (hetero)aryl groups successfully underwent migration to the backbone (C2) position to provide previously inaccessible bicyclic molecules, and the ester group of the product can serve as a handle for downstream manipulation, thus offering opportunities to rapidly build up molecular complexity and access new sp3-rich chemical space.

A Short Synthesis of Ergot Alkaloids and Evaluation of the 5-HT1/2 Receptor Selectivity of Lysergols and Isolysergols.

Key transformations in a four-step synthesis of the ergot alkaloid scaffold include a novel cesium carbonate-mediated hydrogen autotransfer alkylation to generate the C(3)-C(4) bond and an intramolecular Heck reaction that directly establishes the C(9)-C(10) alkene of methyl lysergate. An ester reduction and a streamlined experimental procedure establish a readily scalable, expedient total synthesis of all four stereoisomers of lysergol and isolysergol, including the previously unknown (-)-lysergol, for pharmacological evaluation at 5-HT1A and 5HT2A,B,C receptors. A bicyclic scaffold is also characterized for the first time in the intramolecular Heck coupling.

Bioinspired Asymmetric Total Synthesis of Emeriones A–C**

AbstractWe report asymmetric bioinspired total syntheses of the fungal metabolites emeriones A–C via stereoselective oxidations of two bicyclo[4.2.0]octadiene diastereomers. The central bicyclic scaffolds are prepared in an 8π/6π electrocyclization cascade of a stereodefined pentaene, which contains the fully assembled side chains of the emeriones. The anti‐aldol side chain is made using a Paterson‐aldol addition, and the epoxide of the dioxabicyclo[3.1.0]hexane side chain via ring‐closure onto an oxidized acetal. Our work has enabled the structural revision of emerione C, and resulted in the synthesis of a “missing” family member, which we call emerione D. DFT calculations identified two methyl groups that govern torquoselectivity in the 8π/6π cascade.

Bicyclic thiaspiro[4.n]alkanones: Investigating their total stereochemistry achieved by the catalyst-free sulfa-Michael reaction

A series of twenty-two examples of bicyclic 1-aryl-4‑hydroxy-2-thiaspiro[4.n]alkanones (3, 4), where aryl = phenyl, 4-CH3OC6H4, 4-NO2C6H4, 4-FC6H4, 4-ClC6H4, 4-CH3C6H4,1-naphthyl, 4-N(CH3)2C6H4, and n = 4, 5 were obtained from a catalyst-free sulfa-Michael reaction in refluxing ethanol as a solvent at up to 98% of yield, starting from the readily available 2-arylidene-cycloalkanones (1) and 1,4-dithian-2,5-diol (2) as the precursors. Vinyl ketones 1 were synthesized by reacting simple cyclopentanone and cyclohexanone with aryl aldehydes through well-established procedures. Subsequently, efforts were devoted to isolation, structural characterization by NMR and SC-XRD techniques, and configuration assignment to identify diastereomers containing multiple chiral centers at the bicyclic scaffolds (3, 4), which were presented, discussed, and compared to precedent studies for 1-tetralone and 1-indanone analogues.

Bioinspired Asymmetric Total Synthesis of Emeriones A-C.

We report asymmetric bioinspired total syntheses of the fungal metabolites emeriones A–C via stereoselective oxidations of two bicyclo[4.2.0]octadiene diastereomers. The central bicyclic scaffolds are prepared in an 8π/6π electrocyclization cascade of a stereodefined pentaene, which contains the fully assembled side chains of the emeriones. The anti‐aldol side chain is made using a Paterson‐aldol addition, and the epoxide of the dioxabicyclo[3.1.0]hexane side chain via ring‐closure onto an oxidized acetal. Our work has enabled the structural revision of emerione C, and resulted in the synthesis of a “missing” family member, which we call emerione D. DFT calculations identified two methyl groups that govern torquoselectivity in the 8π/6π cascade.

Synthesis of β2,2-Amino Acids by Stereoselective Alkylation of Isoserine Derivatives Followed by Nucleophilic Ring Opening of Quaternary Sulfamidates.

Chiral bicyclic N,O-acetal isoserine derivatives have been synthesized by an acid-catalyzed tandem N,O-acetalization/intramolecular transcarbamoylation reaction between conveniently protected l-isoserine and 2,2,3,3-tetramethoxybutane. The delicate balance of the steric interactions between the different functional groups on each possible diastereoisomer controls their thermodynamic stability and hence the experimental product distribution. These chiral isoserine derivatives undergo diastereoselective alkylation at the α position, proceeding with either retention or inversion of the configuration depending on the relative configuration of the stereocenters. Quantum mechanical calculations revealed that a concave-face alkylation is favored due to smaller torsional and steric interactions at the bicyclic scaffold. This synthetic methodology gives access to chiral β2,2-amino acids, attractive compounds bearing a quaternary stereocenter at the α position with applications in peptidomimetic and medicinal chemistry. Thus, enantiopure α-alkylisoserine derivatives were produced upon acidic hydrolysis of these alkylated scaffolds. In addition, α-benzylisoserine was readily transformed into a five-membered ring cyclic sulfamidate, which was ring opened regioselectively with representative nucleophiles to yield other types of enantiopure β2,2-amino acids such as α-benzyl-α-heterofunctionalized-β-alanines and α-benzylnorlanthionine derivatives.

Modulating the selectivity of inhibitors for prolyl oligopeptidase inhibitors and fibroblast activation protein-α for different indications

We have previously described several different chemical series of bicyclic prolyl oligopeptidase (POP) inhibitors as probes for neurodegenerative diseases that demonstrated nanomolar activity in vitro and submicromolar activity in cellulo. The more recent implication of POP in cancer, together with homologous fibroblast activation protein α (FAP), implicated in tumor growth, led us to consider developing POP/FAP dual inhibitors as a promising strategy for the development of cancer therapeutics. At this stage, we thought to evaluate the requirements for selectivity of inhibitors for POP over FAP and to evaluate molecular platforms that would enable the development of selective POP and dual POP/FAP inhibitors. We report herein docking-guided design of a new bicyclic scaffold and synthesis of both covalent and non-covalent bicyclic inhibitors. Biological evaluation of first-of-their-kind [4.3.0] bicyclic compounds confirmed that reactive groups, or covalent warheads, are required for inhibitor activity. This work ultimately led to one scaffold yielding new POP-selective inhibitors and a dual inhibitor equipotent to the only drug targeting FAP and POP that ever reached clinical trials.

Multiparameter Optimization of Naphthyridine Derivatives as Selective α5-GABAA Receptor Negative Allosteric Modulators.

The discovery and characterization of novel naphthyridine derivatives with selective α5-GABAAR negative allosteric modulator (NAM) activity are disclosed. Utilizing a scaffold-hopping strategy, fused [6 + 6] bicyclic scaffolds were designed and synthesized. Among these, 1,6-naphthyridinones were identified as potent and selective α5-GABAAR NAMs with metabolic stability, cardiac safety, and beneficial intellectual property (IP) issues. Relocation of the oxo acceptor function and subsequent modulation of the physicochemical properties resulted in novel 1,6-naphthyridines with improved profile, combining good potency, selectivity, ADME, and safety properties. Besides this, compound 20, having the most balanced profile, provided in vivo proof of concept (POC) for the new scaffold in two animal models of cognitive impairment associated with schizophrenia (CIAS).

Synthesis of 3-epi-Hypatulin B Featuring a Late-Stage Photo-Oxidation in Flow.

A synthesis of 3-epi-hypatulin B, a highly oxygenated and densely functionalized bicyclic scaffold, is reported. The carbon skeleton was prepared by functionalization of a cyclopentanone and an intramolecular Mukaiyama aldol reaction. Highlights include a late-stage photo-oxidation of a methoxyallene to provide an ester group. The problems encountered in the batch process were solved by translation into a flow protocol. Our synthesis highlights the value of flow chemistry to enable challenging late-stage transformations in natural product synthesis.

Radical SAM-dependent ether crosslink in daropeptide biosynthesis

Darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP), which possesses potent activity against various Gram-negative bacteria. Darobactin features a highly unique bicyclic scaffold, consisting of an ether crosslink between two Trp residues and a C–C crosslink between a Lys and a Trp. Here we report in vivo and in vitro activity of darobactin synthase DarE. We show DarE is a radical S-adenosylmethionine (rSAM) enzyme and is solely responsible for forming the bicyclic scaffold of darobactin. DarE mainly produced the ether-crosslinked product in vitro, and when the assay was performed in H218O, apparent 18O incorporation was observed into the ether-crosslinked product. These observations suggested an rSAM-dependent process in darobactin biosynthesis, involving a highly unusual oxygen insertion step from a water molecule and subsequent O–H and C–H activations. Genome mining analysis demonstrates the diversity of darobactin-like biosynthetic gene clusters, a subclade of which likely encode monocyclic products with only an ether linkage. We propose the name daropeptide for this growing family of ether-containing RiPPs produced by DarE enzymes.

Regiocontrolled Dimerization of Densely Functionalized 1,6-Dihydropyridines for the Biomimetic Synthesis of a Halicyclamine-type Scaffold by Preventing Disproportionation.

The biomimetic dimerization of 1,6-dihydropyridines (DHPs) remains a daunting challenge due to competitive disproportionation pathways. Herein we report the regioselective dimerization of densely functionalized 1,6-DHPs that allow direct access to the bis-nitrogen bicyclic scaffold of halicyclamines. Disproportionation triggered by the hydride shift of 1,6-DHP was suppressed by the use of geminal disubstituted substrates. Installation of an electron-withdrawing substituent at the C3 position was demonstrated to be crucial for facilitating biomimetic dimerization under metal-free conditions, with exquisite control of regioselectivity at ambient temperature. Our approach, featuring an appropriately functionalized and substantially stabilized substrate rather than merely adopting the highly reactive and labile hypothetical biosynthetic intermediate, allowed gram-scale and atom-economical synthesis of the bis-nitrogen bicyclic scaffold. Furthermore, conversion of a series of 1,6-DHPs provided mechanistic insights by circumventing the competitive disproportionation reaction. This revealed not only the innate reactivity of the conjugate diene system for [4 + 2] cycloaddition but also the reversibility of the dimerization reaction with multiple cationic intermediates in equilibrium.

The azulene scaffold from a medicinal chemist's perspective: Physicochemical and in vitro parameters relevant for drug discovery

Azulene is a bicyclic scaffold rarely applied in medicinal chemistry. Here we report physicochemical and in vitro parameters relevant for drug discovery for a series of diversely substituted azulenes. We synthesized and characterized several scaffold hopping series of analogously substituted azulenes, indoles and naphthalenes. This enabled a comparison of azulene with the more common scaffolds indole and naphthalene. Our data indicates that undesirably low photostability of azulenes is restricted to certain substitution patterns. Generally, we conclude that azulene is an underused lipophilic bicycle and should be considered as a valuable complement to the collection of medicinal chemistry scaffolds.

Applying a Bioisosteric Replacement Strategy in the Discovery and Optimization of Mesoionic Pyrido[1,2-a]pyrimidinone Insecticides: A Review.

Mesoionic pyrido[1,2-a]pyrimidinones are a unique class of heterocyclic compounds. Compounds from this class with a n-propyl group substituted at the 1 position of the mesoionic core were discovered with interesting insecticidal activity in our screen. In this overview, we showcase how a bioisosteric replacement strategy was applied during the discovery and optimization of this class of compounds. Through exploring various substituents at the 1 position, evaluating a variety of mesoionic bicyclic ring scaffolds, and examining substituents on the phenyl group at the 3 position of the mesoionic core as well as substituents on the mesoionic ring skeleton, many compounds were discovered with excellent hopper activity or potent activity against a wide range of Lepidoptera. Ultimately, dicloromezotiaz was identified for commercial development to control a broad spectrum of lepidopteran pests.

The Role of the Fused Ring in Bicyclic Triazolium Organocatalysts: Kinetic, X-ray, and DFT Insights.

Bicyclic triazolium scaffolds are widely employed in N-heterocyclic carbene (NHC) organocatalysis. While the incorporation of a fused ring was initially for synthetic utility in accessing chiral, modular triazolyl scaffolds, recent results highlight the potential for impact upon reaction outcome with the underpinning origins unclear. The common first step to all triazolium-catalyzed transformations is C(3)-H deprotonation to form the triazolylidene NHC. Herein, we report an analysis of the impact of size of the fused (5-, 6-, and 7-membered, n = 1, 2, and 3, respectively) ring on the C(3) proton transfer reactions of a series of bicyclic triazolium salts. Rate constants for the deuteroxide-catalyzed C(3)-H/D-exchange of triazolium salts, kDO, were significantly influenced by the size of the adjacent fused ring, with the kinetic acidity trend, or protofugalities, following the order kDO (n = 1) > kDO (n = 2) ≈ kDO (n = 3). Detailed analyses of X-ray diffraction (XRD) data for 20 triazolium salts (including 16 new structures) and of computational data for the corresponding triazolylidene NHCs provide insight on structural effects of alteration of fused ring size. In particular, changes in internal triazolyl NCN angle and positioning of the most proximal CH2 with variation in fused ring size are proposed to influence the experimental protofugality order.

Organocatalyst Design for the Stereoselective Annulation towards Bicyclic Diketones and Analogues

The Wieland–Miescher ketone, Hajos–Parrish–Eder–Sauer–Wiechert ketone, and their analogues are bicyclic diketones essential as building blocks for the synthesis of several natural and bioactive molecules. For this reason, since 1971, when Hajos and Parrish and Eder, Sauer, and Wiechert reported the stereoselective synthesis of these compounds promoted by L-proline, numerous methodologies and organocatalysts have been studied over the years with the aim of identifying increasingly efficient asymmetrical syntheses of these bicyclic ketones. This review will outline the methodological and stereochemical features of the organocatalytic stereoselective synthesis of these bicyclic scaffolds based on the different organocatalysts employed from 1971 until today. Particular emphasis will be given to the structural features of the catalysts and to the reaction conditions.

A specialized role played by a redox cofactor

The redox cofactor β-nicotinamide adenine dinucleotide (NAD) has been revealed to serve as a building block for the biosynthesis of an alkaloid natural product, altemicidin. The biosynthetic pathway investigation identified a unique pyridoxal pyrophosphate (PLP)-dependent enzyme that utilizes NAD and S-adenosylmethionine (SAM) to build the bicyclic alkaloid scaffold, opening the door for biosynthetic studies of NAD-derived natural products.

Methyl nitrate energetic compounds based on bicyclic scaffolds of furazan-isofurazan (isoxazole): syntheses, crystal structures and detonation performances.

Two energetic bicyclic scaffolds (furazan–isoxazole and furazan–1,3,4-oxadiazole) were constructed via different cyclization reactions. Based on the energetic bicyclic scaffolds, the energetic compounds, 3-(4-nitraminofurazan-3-ly)-isoxazole-5-methylnitrate 1c and 5-(4-nitraminofurazan-3-ly)-1,3,4-oxadiazole-2-methylnitrate 2c, were designed and synthesized in good yields. Because of the acidity of nitramine, the corresponding energetic ionic salts, ammonium 3-(4-nitraminofurazan-3-ly)isoxazole-5-methylnitrate 1d and ammonium 5-(4-nitraminofurazan-3-ly)-1,3,4-oxadiazole-2-methylnitrate 2e, were also obtained and well characterized, their structures were further determined by X-ray single crystal diffraction. To have a better understanding of the structure–property relationships of furazan-bicyclic scaffolds and nitrate groups, their thermal behaviors, detonation performances and the sensitivities were investigated via differential scanning calorimetry (DSC), ESP analysis, Hirshfeld surfaces calculation, EXPLO5 program and BAM standard techniques. Compared with those of ammonium 5-(4-nitraminofurazan-3-ly)-1,2,4-oxadiazole-2-methylnitrate 3e, the results show that all these methyl nitrate energetic compounds based on bicyclic scaffolds of furazan–isofurazan exhibit good detonation performances and extraordinary insensitivities. As supported by experimental and theoretical data, the formation of energetic ionic salts causes an increase of the weak interactions, significantly improving the thermal performance over 110 °C.