Silver(I)-Catalyzed Synthesis of Cuneanes from Cubanes and their Investigation as Isosteres

Enantioselective photocatalytic synthesis of bicyclo[2.1.1]hexanes as ortho-disubstituted benzene bioisosteres with improved biological activity

1,5-Disubstituted bicyclo[2.1.1]hexanes are bridged scaffolds with well-defined exit vectors that are becoming increasingly popular building blocks in medicinal chemistry because they are saturated bioisosteres of ortho-substituted phenyl rings. Here we have developed a Lewis-acid-catalysed [2 + 2] photocycloaddition to obtain these motifs as enantioenriched scaffolds, providing an efficient approach for their incorporation in a variety of drug analogues. Retention of the biological activity of the bicyclo[2.1.1]hexane-containing analogues in the specific proteins targeted by the original drugs has confirmed the suitability of this moiety to serve as a bioisostere of ortho-substituted phenyl rings. Moreover, we have studied the potential of the different enantiomers of the drug analogues to selectively induce cytotoxicity in a panel of tumour cell lines, observing markedly differential effects for the two enantiomers and a substantial improvement over the corresponding sp2-based drugs. This showcases that the control of the absolute configuration and tridimensionality of the drug analogue has a large impact on its biological properties.

Catalytic Asymmetric Synthesis of Chiral Caged Hydrocarbons as Arenes Bioisosteres

The utilization of caged hydrocarbons as bioisosteres for arenes, especially the phenyl ring, in bioactive compounds has resulted in significant enhancements in potency, solubility, and metabolic stability. These improvements highlight the potential of C(sp3)-rich polycyclic scaffolds as a promising motif for the development of drug candidates. However, this strategy has also increased the structural complexity of these molecules, posing synthetic challenges in controlling the chirality of caged and highly decorated bioactive scaffolds. Over the past two years, remarkable progress has been achieved in catalytic asymmetric methodologies for the synthesis of caged hydrocarbons, significantly advancing their utility in chiral drug discovery and development. This minireview provides a comprehensive summary of recent breakthroughs in the catalytic asymmetric synthesis of chiral caged hydrocarbons, encompassing bicyclo[n.1.1]alkanes, cubanes, and related three-dimensional scaffolds. Additionally, we highlight the intriguing applications of enantiomerically pure caged hydrocarbons in biological studies. It is anticipated that this minireview will inspire further advancements in the enantioselective synthesis of these pharmaceutically valuable caged hydrocarbons.

3-Oxabicyclo[3.1.1]heptane as an Isostere of meta-Benzene

3-Oxabicyclo[3.1.1]heptanes were designed as saturated isosteres of meta-benzene. Crystallographic analysis revealed that these structures and meta-benzene have identical geometric properties. Replacement of the central benzene ring in the anticancer drug Sonidegib with 3-oxabicyclo[3.1.1]heptane provided a patent-free analogue with a nanomolar potency, reduced lipophilicity, and improved water solubility (>500%).

Gold-Catalyzed 1,2-Rearrangement on Benzene Triggered by a Transient Dearomative Claisen Rearrangement

1,2-Migration on arenes represents a powerful transformation, because of its chemical skeleton and exit vector editing ability. However, the corresponding dearomative mediated 1,2-migration on arene was ignored for decades, despite tremendous effort being devoted to develop the dearomative reaction, which mainly capitalized on breaking the planarity for three-dimensional diversification. Here, we report on the gold-catalyzed 1,2-rearrangement on benzene by the transient dearomatization of high-resonance energy benzene. This functional transposition strategy enabled rapid access to several precursors of extended π-conjugated molecules, showcasing its potential applications in materials sciences.

Expanding the Repertoire of Large Scaffolds with Syn and Anti Macrocyclic Metacyclophanes

Understanding how changes in structure translate to changes in molecular shape is key to catalyst optimization and molecular design in medicinal chemistry and materials. One key contributor to the molecular shape is the relative orientation of substituents on a scaffold. Macrocyclic metacyclophanes display their two arenes in a parallel or antiparallel fashion, resulting in anti or syn conformations that lead to disparate relative orientations of the aryl substituents. This work reports the synthesis of new 14- and 16-membered metacyclophanes and the elucidation of their anti/syn preferences by 1H NMR and computational conformational analysis. Most metacyclophanes studied herein display a strong anti or syn preference and, thus, have well-defined substituent orientations. We propose that anti/syn conformational preferences arise from the minimization of torsional strain along the backbone of the macrocycle, which leads to the prediction that metacyclophanes with remote aryl substituents will adopt the same conformation as their unsubstituted counterparts. Exit vector analysis also reveals that anti-metacyclophanes project their substituents into regions in three-dimensional space that are not accessed by other common large scaffolds, e.g., [2.2]paracyclophanes and ferrocenes. This work also demonstrates how ring size and functional groups, two parameters commonly optimized in macrocycle design, can be used to tune molecular shape.

Au-Catalyzed 5C Reaction of Type II Diene-Ynenes toward Dihydrosemibullvalenes: Reaction Development and Mechanistic Study

We report an unexpected gold-catalyzed 5C reaction of type II diene-ynenes to synthesize dihydrosemibullvalenes, which are potential bioisosteres for drug discovery. This 5C reaction occurs through a sequence of elementary reactions of cyclopropanation/Cope rearrangement/carbon shift/cyclopropanation/C-H insertion (shortened here as the 5C reaction), supported by quantum chemistry calculations. Mechanistic studies have also been applied to answer why type-II diene-ynenes cannot access seven-membered carbocycles-embedded bridged molecules under the gold catalysis, finding that the chair-like Cope rearrangement transition state (not the traditional boat-like transition state) is the key to the change of regiochemistry.

Germanyl triazoles as a platform for CuAAC diversification and chemoselective orthogonal cross-coupling

We report the synthesis of germanyl triazoles formed via a copper-catalysed azide-alkyne cycloaddition (CuAAC) of germanyl alkynes. The reaction is often high yielding, functional group tolerant, and compatible with complex molecules. The installation of the Ge moiety enables further diversification of the triazole products, including chemoselective transition metal-catalysed cross-coupling reactions using bifunctional boryl/germyl species.

1,3-Bishomocubane: a kinetic rock, a thermodynamic powerhouse and a compelling chiral synthetic scaffold

Over the last several decades, saturated polycyclic cage compounds have remained a point of interest for organic chemists because of their unique characteristics and reactivity. For the first time, a detailed analysis of the synthesis, properties and transformations of 1,3-bishomocubanes, which fall under the rare category of chiral cage compounds, is provided in this article. This review which also includes the authors' work in this area over the last decade is expected to serve as a valuable resource for chemists interested in the fascinating chemistry and properties of polycyclic cage compounds.

Zinc-Catalyzed Enantioselective Formal (3+2) Cycloadditions of Bicyclobutanes with Imines: Catalytic Asymmetric Synthesis of Azabicyclo[2.1.1]hexanes

The cycloaddition reaction involving bicyclo[1.1.0]butanes (BCBs) offers a versatile and efficient synthetic platform for producing C(sp3)-rich rigid bridged ring scaffolds, which act as phenyl bioisosteres. However, there is a scarcity of catalytic asymmetric cycloadditions of BCBs to fulfill the need for enantioenriched saturated bicycles in drug design and development. In this study, an efficient synthesis of valuable azabicyclo[2.1.1]hexanes (aza-BCHs) by an enantioselective zinc-catalyzed (3+2) cycloadditions of BCBs with imines is reported. The reaction proceeds effectively with a novel type of BCB that incorporates a 2-acyl imidazole group and a diverse array of alkynyl- and aryl-substituted imines. The target aza-BCHs, which consist of α-chiral amine fragments and two quaternary carbon centers, are efficiently synthesized with up to 94 % and 96.5:3.5 er under mild conditions. Experimental and computational studies reveal that the reaction follows a concerted nucleophilic ring-opening mechanism of BCBs with imines. This mechanism is distinct from previous studies on Lewis acid-catalyzed cycloadditions of BCBs.

Catalytic asymmetric synthesis of meta benzene isosteres

Although aromatic rings are common elements in pharmaceutically active compounds, the presence of these motifs brings several liabilities with respect to the developability of a drug1. Nonoptimal potency, metabolic stability, solubility and lipophilicity in pharmaceutical compounds can be improved by replacing aromatic rings with non-aromatic isosteric motifs2. Moreover, whereas aromatic rings are planar and lack three-dimensionality, the binding pockets of most pharmaceutical targets are chiral. Thus, the stereochemical configuration of the isosteric replacements may offer an added opportunity to improve the affinity of derived ligands for target receptors. A notable impediment to this approach is the lack of simple and scalable catalytic enantioselective syntheses of candidate isosteres from readily available precursors. Here we present a previously unknown palladium-catalysed reaction that converts hydrocarbon-derived precursors to chiral boron-containing nortricyclanes and we show that the shape of these nortricyclanes makes them plausible isosteres for meta disubstituted aromatic rings. With chiral catalysts, the Pd-catalysed reaction can be accomplished in an enantioselective fashion and subsequent transformation of the boron group provides access to a broad array of structures. We also show that the incorporation of nortricyclanes into pharmaceutical motifs can result in improved biophysical properties along with stereochemistry-dependent activity. We anticipate that these features, coupled with the simple, inexpensive synthesis of the functionalized nortricyclane scaffold, will render this platform a useful foundation for the assembly of new biologically active agents.

Three-dimensional saturated C(sp3)-rich bioisosteres for benzene

Benzenes, the most ubiquitous structural moiety in marketed small-molecule drugs, are frequently associated with poor 'drug-like' properties, including metabolic instability, and poor aqueous solubility. In an effort to overcome these limitations, recent developments in medicinal chemistry have demonstrated the improved physicochemical profiles of C(sp3)-rich bioisosteric scaffolds relative to arenes. In the past two decades, we have witnessed an exponential increase in synthetic methods for accessing saturated bioisosteres of monosubstituted and para-substituted benzenes. However, until recent discoveries, analogous three-dimensional ortho-substituted and meta-substituted biososteres have remained underexplored, owing to their ring strain and increased s-character hybridization. This Review summarizes the emerging synthetic methodologies to access such saturated motifs and their impact on the application of bioisosteres for ortho-substituted, meta-substituted and multi-substituted benzene rings. It concludes with a perspective on the development of next-generation bioisosteres, including those within novel chemical space.

2-Oxabicyclo[2.1.1]hexanes: Synthesis, Properties, and Validation as Bioisosteres of ortho- and meta-Benzenes

We have developed a general and practical approach towards 2-oxabicyclo[2.1.1]hexanes with two and three exit vectors via an iodocyclization reaction. The obtained compounds have been easily converted into the corresponding building blocks for use in medicinal chemistry. 2-Oxabicyclo[2.1.1]hexanes have been incorporated into the structure of five drugs and three agrochemicals, and validated biologically as bioisosteres of ortho- and meta-benzenes.

(Bio)isosteres of ortho- and meta-substituted benzenes

Saturated bioisosteres of substituted benzenes offer opportunities to fine-tune the properties of drug candidates in development. Bioisosteres of para-benzenes, such as those based on bicyclo[1.1.1]pentane, are now very common and can be used to increase aqueous solubility and improve metabolic stability, among other benefits. Bioisosteres of ortho- and meta-benzenes were for a long time severely underdeveloped by comparison. This has begun to change in recent years, with a number of potential systems being reported that can act as bioisosteres for these important fragments. In this review, we will discuss these recent developments, summarizing the synthetic approaches to the different bioisosteres as well as the impact they have on the physiochemical and biological properties of pharmaceuticals and agrochemicals.

Assessing the rigidity of cubanes and bicyclo(1.1.1)pentanes as benzene bioisosteres

Aromatic rings are critical core substructures in the majority of pharmaceutical compounds. There is much recent interest in replacing aromatic structures with saturated bioisosteres of benzene, which are generally fused or bridged ring systems. These bioisosteres often show improved solubility properties compared to benzene, and may also undergo fewer unwanted metabolic processes. One key reason why aromatic rings have proven so successful in drug design is their rigidity. This paper uses molecular dynamics simulations supported by crystallographic data to assess the rigidity of bicyclopentane and cubane ring systems as two of the most common benzene bioisosteres and compares this to benzene. Whilst a benzene ring is shown to be more flexible than these two bioisosteres in terms of its dihedral ring flexibility, substituents around the ring tend to behave in a much more similar way in both benzene and the bioisosteric systems.

Computational Research on Ag(I)-Catalyzed Cubane Rearrangement: Mechanism, Metal and Counteranion Effect, Ligand Engineering, and Post-Transition-State Desymmetrization

Ag(I) salts have demonstrated superior catalytic activity in the cubane-cuneane rearrangement. This research presents a comprehensive mechanistic investigation using high-level computations. The reaction proceeds via oxidative addition (OA) of Ag(I) to the C-C bond, followed by C-Ag bond cleavage and subsequent dynamically concerted carbocation rearrangement. The OA of Ag(I) exhibits significant more electrophilic nature than classical transition metal-induced OA, and the superior catalytic activity of Ag(I) is attributed to the accessibility of a highly electrophilic "bare" Ag+ center and a relatively weak Ag-C bond. However, the highly Lewis acidic nature of the Ag(I) center limits the substrate scope. To address this problem, ligand and counteranion screening was conducted, revealing that chiral biarylether ligands in combination with BF4- as the counteranion offer both enhanced reactivity and improved chemoselectivity while suppressing the Lewis acidity. Additionally, quasi-classical molecular dynamics simulations indicate the possibility of a novel desymmetrization pathway through post-transition-state dynamics in the biarylether-Ag(I)-BF4- system, thereby providing a potential avenue for enantioselective cuneane synthesis.

Spiro[3.3]heptane as a Saturated Benzene Bioisostere

The spiro[3.3]heptane core, with the non-coplanar exit vectors, was shown to be a saturated benzene bioisostere. This scaffold was incorporated into the anticancer drug sonidegib (instead of the meta-benzene), the anticancer drug vorinostat (instead of the phenyl ring), and the anesthetic drug benzocaine (instead of the para-benzene). The patent-free saturated analogs obtained showed a high potency in the corresponding biological assays.

Bicyclo[m.n.k]alkane Building Blocks as Promising Benzene and Cycloalkane Isosteres: Multigram Synthesis, Physicochemical and Structural Characterization

Electrophilic double bond functionalization - intramolecular enolate alkylation sequence was used to obtain a series of bridged and fused bicyclo[m.n.k]alkane derivatives (i. e., bicyclo[4.1.1]octanes, bicyclo[2.2.1]heptanes, bicyclo[3.2.1]octanes, bicyclo[3.1.0]hexanes, and bicyclo[4.2.0]heptanes). The scope and limitations of the method were established, and applicability to the multigram synthesis of target bicyclic compounds was illustrated. Using the developed protocols, over 50 mono- and bifunctional building blocks relevant to medicinal chemistry were prepared. The synthesized compounds are promising isosteres of benzene and cycloalkane rings, which is confirmed by their physicochemical and structural characterization (pKa , LogP, and exit vector parameters (EVP)). "Rules of thumb" for the upcoming isosteric replacement studies were proposed.

Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis

Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod-SELEX) or after the in vitro selection process (post-SELEX). In order to reduce the complexity and workload of the post-SELEX modification of aptamers, we have evaluated the possibility of improving a previously reported, chemically modified aptamer by combining enzymatic synthesis and nucleotides bearing bioisosteres of the parent cubane side-chains or substituted cubane moieties. This method lowers the synthetic burden often associated with post-SELEX approaches and allowed to identify one additional sequence that maintains binding to the PvLDH target protein, albeit with reduced specificity. In addition, while bioisosteres often improve the potency of small molecule drugs, this does not extend to chemically modified aptamers. Overall, this versatile method can be applied for the post-SELEX modification of other aptamers and functional nucleic acids.

A Photochemical Strategy for the Conversion of Nitroarenes into Rigidified Pyrrolidine Analogues

Bicyclic amines are important motifs for the preparation of bioactive materials. These species have well-defined exit vectors that enable accurate disposition of substituents toward specific areas of chemical space. Of all possible skeletons, the 2-azabicyclo[3.2.0]heptane framework is virtually absent from MedChem libraries due to a paucity of synthetic methods for its preparation. Here, we report a modular synthetic strategy that utilizes nitroarenes as flat and easy-to-functionalize feedstocks for the assembly of these sp3-rich materials. Mechanistically, this approach exploits two concomitant photochemical processes that sequentially ring-expand the nitroarene into an azepine and then fold it into a rigid bicycle pyrroline by means of singlet nitrene-mediated nitrogen insertion and excited-state-4π electrocyclization. A following hydrogenolysis provides, with full diastereocontrol, the desired bicyclic amine derivatives whereby the aromatic substitution pattern has been translated into the one of the three-dimensional heterocycle. These molecules can be considered rigid pyrrolidine analogues with a well-defined orientation of their substituents. Furthermore, unsupervised clustering of an expansive virtual database of saturated N-heterocycles revealed these derivatives as effective isosteres of rigidified piperidines. Overall, this platform enables the conversion of nitroarene feedstocks into complex sp3-rich heterocycles of potential interest to drug development.

Scaffold Editing of Cubanes into Homocubanes, Homocuneanes via Cuneanes

The selective synthesis of cage-type hydrocarbons through the editing of the highly symmetric molecule cubane can be anticipated as one of the efficient approaches. In this paper, we identify a catalyst that facilitates the efficient scaffold isomerization of cubanes into homocubanes. This approach, which involves the direct synthesis of homocubanol esters, is promising as a novel method for the synthesis of phenoxy bioisosteres. Additionally, we observed that the isomerization of 1,4-bis(acyloxymethl)cubane results in the generation of both D2 - and C2 -symmetrical bishomocubanes. The same catalyst was also applied to the isomerization of acyloxymethylcuneanes, producing homocuneanol esters.

C(sp2)-H cyclobutylation of hydroxyarenes enabled by silver-π-acid catalysis: diastereocontrolled synthesis of 1,3-difunctionalized cyclobutanes

Ring-opening of bicyclo[1.1.0]butanes (BCBs) is emerging as a powerful strategy for 1,3-difunctionalized cyclobutane synthesis. However, reported radical strain-release reactions are typically plagued with diastereoselectivity issues. Herein, an atom-economic protocol for the highly chemo- and diastereoselective polar strain-release ring-opening of BCBs with hydroxyarenes catalyzed by a π-acid catalyst AgBF4 has been developed. The use of readily available starting materials, low catalyst loading, high selectivity (up to >98 : 2 d.r.), a broad substrate scope, ease of scale-up, and versatile functionalizations of the cyclobutane products make this approach very attractive for the synthesis of 1,1,3-trisubstituted cyclobutanes. Moreover, control experiments and theoretical calculations were performed to illustrate the reaction mechanism and selectivity.

Preparation of 3,5-Methanobenzo[b]azepines: An sp3-Rich Quinolone Isostere

The replacement of the aromatic ring in bioactive compounds with saturated bioisosteres has become a popular tactic to obtain novel structures with improved physicochemical profiles. In this paper, we describe an efficient synthesis of 3,5-methanobenzo[b]azepine analogues and suggest them as isosteres of quinolones. Quinolones are heteroaromatic, flat rings and considered as privileged scaffolds. An isosteric version of this scaffold with more 3D character would offer new options to expand their use.