The cubane paradigm in bioactive molecule discovery: further scope, limitations and the cyclooctatetraene complement

Tetraasteranes as homologues of cubanes: effective scaffolds for drug discovery

Classical hydrocarbon scaffolds have long assisted in bringing new molecules to the market for a variety of applications, but one notable omission is that of tetraasteranes, which are homologues of cubanes belonging to a class of polycyclic hydrocarbon cage compounds. Tetraasteranes exhibit potential as scaffolds in drug discovery due to their identical cyclobutane structures and rigid conformation resembling cubanes. Based on the studies of the physical and chemical properties of tetraasteranes by density functional theory, three series of compounds were designed as homologues of cubanes by the substitution of cubane scaffolds in pharmaceuticals with tetraasteranes. Their potential for pharmaceutical applications was evaluated in silico by molecular docking and dynamics simulations. Their pharmacokinetic and physicochemical properties were studied by the ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The results indicate that tetraasteranes may be scaffolds as novel bioisosteres of cubanes, as well as hydrogen bond donors or acceptors, which enhance the affinity between ligands and receptors with more stable binding behavior and feasible tolerability in ADMET. All these findings provide new opportunities for tetraasteranes to serve as effective pharmaceutical scaffolds for drug discovery and to accelerate the drug discovery process by repurposing both new and old commercial compounds.

Simplified Nomenclature and Projection Diagrams of Chiral Cubane Analogs

A simplified nomenclature for chiral cubane analogs is proposed where analogs with a clockwise systematic continuous numbering of the cubane core are designated as (C)-, and analogs with an anticlockwise continuous numbering of the cubane core are designated as (A)-. This method is accurate, allows for the rapid conversion of the chemical name to a structure, and it eliminates the need to designate the stereochemistry of each of the 8 carbons of cubane.

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.

General Synthesis of Conformationally Constrained Noncanonical Amino Acids with C(sp3)-Rich Benzene Bioisosteres

Recent years have seen novel modalities emerge for the treatment of human diseases resulting in an increase in beyond rule of 5 (bRo5) chemical matter. As a result, synthetic innovations aiming to enable rapid access to complex bRo5 molecular entities have become increasingly valuable for medicinal chemists' toolkits. Herein, we report the general synthesis of a new class of noncanonical amino acids (ncAA) with a cyclopropyl backbone to achieve conformational constraint and bearing C(sp3)-rich benzene bioisosteres. We also demonstrate preliminary studies toward utilities of these ncAA as building blocks for medicinal chemistry research.

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.

Biological Evaluation of Isosteric Applicability of 1,3-Substituted Cuneanes as m-Substituted Benzenes Enabled by Selective Isomerization of 1,4-Substituted Cubanes

We herein evaluate a biological applicability of 1,3-substituted cuneanes as an isostere of m-substituted benzenes based on its structural similarity. An investigation of a method to obtain 1,3-substituted cuneanes by selective isomerization of 1,4-substituted cubanes enables this attempt by giving a key synthetic step to obtain a cuneane analogs of pharmaceuticals having m-substituted benzene moiety. Biological evaluation of the synthesized analogs and in silico study of the obtained result revealed a potential usage of cuneane skeleton in medicinal chemistry.

C-H Alkylation of Cubanes via Catalytic Generation of Cubyl Radicals

A catalytic method for the C-H alkylation of cubanes is described. Some hydrogen atom transfer catalysts enable the direct abstraction of a hydrogen atom from the C-H bond of cubanes, followed by conjugate addition of the generated cubyl radicals to electron-deficient alkenes. Synthetic applications of the functionalization method developed are also described.

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.

Applications of Bioisosteres in the Design of Biologically Active Compounds

The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.

Photoinduced Formation of Cubyl Aryl Thioethers and Synthesis of Monocubyl Analogue of Dapsone

1,4-Disubstituted cubyl aryl thioethers were generated from the corresponding iodocubanes and aryl thiolates upon UV irradiation in dimethyl sulfoxide at room temperature. This simple procedure was found to be compatible with a variety of substituted aryl thiolates. This finding paved the way to a synthesis of the monocubyl analogue of dapsone, a key molecule in the treatment of leprosy, also known as Hansen's disease, and of acne.

2-Oxabicyclo[2.2.2]octane as a new bioisostere of the phenyl ring

The phenyl ring is a basic structural element in chemistry. Here, we show the design, synthesis, and validation of its new saturated bioisostere with improved physicochemical properties - 2-oxabicyclo[2.2.2]octane. The design of the structure is based on the analysis of the advantages and disadvantages of the previously used bioisosteres: bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane, and cubane. The key synthesis step is the iodocyclization of cyclohexane-containing alkenyl alcohols with molecular iodine in acetonitrile. 2-Oxabicyclo[2.2.2]octane core is incorporated into the structure of Imatinib and Vorinostat (SAHA) drugs instead of the phenyl ring. In Imatinib, such replacement leads to improvement of physicochemical properties: increased water solubility, enhanced metabolic stability, and reduced lipophilicity. In Vorinostat, such replacement results in a new bioactive analog of the drug. This study enhances the repertoire of available saturated bioisosteres of (hetero)aromatic rings for the use in drug discovery projects.

Synthesis of polysubstituted bicyclo[2.1.1]hexanes enabling access to new chemical space

Saturated bridged-bicyclic compounds are currently under intense investigation as building blocks for pharmaceutical drug design. However, the most common methods for their preparation only provide access to bridgehead-substituted structures. The synthesis of bridge-functionalised species is highly challenging but would open up many new opportunities for molecular design. We describe a photocatalytic cycloaddition reaction that provides unified access to bicyclo[2.1.1]hexanes with 11 distinct substitution patterns. Bridge-substituted structures that represent ortho-, meta-, and polysubstituted benzene bioisosteres, as well as those that enable the investigation of chemical space inaccessible to aromatic motifs can all be prepared using this operationally simple protocol. Proof-of-concept examples of the application of the method to the synthesis of saturated analogues of biorelevant trisubstituted benzenes are also presented.

About Perfluoropolyhedranes, Their Electron-Accepting Ability and Questionable Supramolecular Hosting Capacity

Polyhedral molecules are appealing for their eye-catching architecture and distinctive chemistry. Perfluorination of such, often greatly strained, compounds is a momentous challenge. It drastically changes the electron distribution, structure and properties. Notably, small high-symmetry perfluoropolyhedranes feature a centrally located, star-shaped low-energy unoccupied molecular orbital that can host an extra electron within the polyhedral frame, thus producing a radical anion, without loss of symmetry. This predicted electron-hosting capacity was definitively established for perfluorocubane, the first perfluorinated Platonic polyhedrane to be isolated pure. Hosting atoms, molecules, or ions in such "cage" structures is, however, all but forthright, if not illusionary, offering no easy access to supramolecular constructs. While adamantane and cubane have fostered numerous applications in materials science, medicine, and biology, specific uses for their perfluorinated counterparts remain to be established. Some aspects of highly fluorinated carbon allotropes, such as fullerenes and graphite, are briefly mentioned for context.

General access to cubanes as benzene bioisosteres

The replacement of benzene rings with sp3-hybridized bioisosteres in drug candidates generally improves pharmacokinetic properties while retaining biological activity1-5. Rigid, strained frameworks such as bicyclo[1.1.1]pentane and cubane are particularly well suited as the ring strain imparts high bond strength and thus metabolic stability on their C-H bonds. Cubane is the ideal bioisostere as it provides the closest geometric match to benzene6,7. At present, however, all cubanes in drug design, like almost all benzene bioisosteres, act solely as substitutes for mono- or para-substituted benzene rings1-7. This is owing to the difficulty of accessing 1,3- and 1,2-disubstituted cubane precursors. The adoption of cubane in drug design has been further hindered by the poor compatibility of cross-coupling reactions with the cubane scaffold, owing to a competing metal-catalysed valence isomerization8-11. Here we report expedient routes to 1,3- and 1,2-disubstituted cubane building blocks using a convenient cyclobutadiene precursor and a photolytic C-H carboxylation reaction, respectively. Moreover, we leverage the slow oxidative addition and rapid reductive elimination of copper to develop C-N, C-C(sp3), C-C(sp2) and C-CF3 cross-coupling protocols12,13. Our research enables facile elaboration of all cubane isomers into drug candidates, thus enabling ideal bioisosteric replacement of ortho-, meta- and para-substituted benzenes.

Photoinduced Diastereoselective Aminoalkylation of Cubanes

The unique properties of rigid, nonconjugated hydrocarbons provide many opportunities to design molecular building blocks for a variety of applications, but the development of suitable conditions for alkylation of cubanes is quite challenging. Herein, a photoinduced method for aminoalkylation of cubanes is reported. The benign conditions reported allow the incorporation of a wide variety of (hetero)arylimine reaction partners with broad functional group tolerance and high diastereoselectivity.

Sustainable Photoinduced Decarboxylative Chlorination Mediated by Halogen Atom Transfer

Chlorinated organic backbones constitute important components in existing biologically active chemicals, and they are extraordinary useful intermediates in organic synthesis. Herein, an operationally simple and sustainable halodecarboxylation protocol via halogen-atom transfer (XAT) as a key step is presented. The method merges a metal-free photoredox system with (diacetoxyiodo)benzene (PIDA) as a hypervalent iodine reagent using 1,2-dihaloethanes as halogen sources to afford haloalkanes in an efficient manner. The sustainability of this protocol is highlighted by an important waste recovery protocol as well as by atom economy and carbon efficiency parameters.

Cage hydrocarbons as linkers in dimeric drug design: Case studies with trimethoprim and tedizolid

The looming threat of a "post-antibiotic era" has been caused by a rapid rise in antibacterial resistance and subsequent depletion of effective antibiotic agents in the clinic. An efficient strategy to address this shortfall lies in the reengineering of pre-existing and commercially available antibiotic drugs. This is exemplified by dimerization, a design concept in which two pharmacophores are covalently linked to form a new chemical entity. The cage hydrocarbons cubane (1), bicyclo[2.2.2]octane (BCO) (2), adamantane (3), and bicyclo[1.1.1]pentane (BCP) (4) present themselves as an attractive family of linkers in this regard. In this report, all four hydrocarbon cages were employed as linkers in a series of dimers based on the commercially available antibiotics trimethoprim and tedizolid. A detailed synthetic roadmap for the protection and deprotection of each pharmacophore is outlined. Several members of the trimethoprim series showed activity on par with that of their trimethoprim progenitor, although this was not the case for the tedizolid series. The design strategy outlined herein highlights the utility of the group as a platform for the rapid and modular construction of future novel antibiotics.

Chiral Auxiliary-Directed Site-Selective Deprotonation of the Cubane Skeleton

The first diastereoselective synthesis of trisubstituted cubanes was achieved using a chiral auxiliary. To establish chirality within the cubane skeleton, at least three substituents must be introduced at the appropriate positions. Ready conversion of cubane carboxylic acid to a chiral amide followed by sequential ortho-selective deprotonations and electrophilic trapping afforded the corresponding 1,2,3-trisubstituted cubanes with high diastereoselectivity. This route opens new possibilities for the preparation of enantio-enriched cubanes.

Advances in nonclassical phenyl bioisosteres for drug structural optimization

The phenyl group is the most prevalent ring system and plays an essential role as a pharmacophore or scaffold in marketed drugs. However, the indiscriminate employment of phenyl is also a major cause of poor physicochemical properties of active molecules. Nonclassical phenyl bioisosteres (NPBs) have emerged as effective replacements for phenyl in structural optimization due to their unique steric structures and physicochemical properties. Herein, the effects of widely reported NPBs on physicochemical properties and biological activities, including bicyclo[1.1.1]pentane (BCP), bicyclo[2.1.1]hexanes (BCH), bicyclo[2.2.2]octane (BCO), cubane (CUB) and closo-carboborane, are reviewed. Issues that require consideration while using NPBs and practical solutions to problems frequently encountered in structural optimization using NPBs are also discussed.

Perfluorocubane-a tiny electron guzzler

Perfluorination gives cubane the capacity to host an extra electron in its inner structure.

Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor

Fluorinated analogs of polyhedral hydrocarbons have been predicted to localize an electron within their cages upon reduction. Here, we report the synthesis and characterization of perfluorocubane, a stable polyhedral fluorocarbon. The key to the successful synthesis was the efficient introduction of multiple fluorine atoms to cubane by liquid-phase reaction with fluorine gas. The solid-state structure of perfluorocubane was confirmed using x-ray crystallography, and its electron-accepting character was corroborated electrochemically and spectroscopically. The radical anion of perfluorocubane was examined by matrix-isolation electron spin resonance spectroscopy, which revealed that the unpaired electron accepted by perfluorocubane is located predominantly inside the cage.

Mechanical Properties of Cubene Crystals

The fullerene family, whose most popular members are the spherical C60 and C70 molecules, has recently added a new member, the cube-shaped carbon molecule C8 called a cubene. A molecular crystal based on fullerenes is called fullerite. In this work, based on relaxational molecular dynamics, two fullerites based on cubenes are described for the first time, one of which belongs to the cubic system, and the other to the triclinic system. Potential energy per atom, elastic constants, and mechanical stress components are calculated as functions of lattice strain. It has been established that the cubic cubene crystal is metastable, while the triclinic crystal is presumably the crystalline phase in the ground state (the potential energies per atom for these two structures are -0.0452 and -0.0480 eV, respectively).The cubic phase has a lower density than the monoclinic one (volumes per cubene are 101 and 97.7 Å3). The elastic constants for the monoclinic phase are approximately 4% higher than those for the cubic phase. The presented results are the first step in studying the physical and mechanical properties of C8 fullerite, which may have potential for hydrogen storage and other applications. In the future, the influence of temperature on the properties of cubenes will be analyzed.

ortho-C-H Acetoxylation of Cubane Enabling Access to Cubane Analogues of Pharmaceutically Relevant Scaffolds

A novel method of introducing an oxygen functionality into a cubane core was developed using a transition-metal-catalyzed directed acetoxylation methodology via C-H activation. The obtained compounds were derivatized into cubane analogues of pharmaceutically relevant structural motifs, namely, acetylsalicylic acid and coumarin motifs, which could potentially act as bioisosteres of these scaffolds.

Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design

The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.

Efficient synthesis of α,β-dichlorinated ketones from α,β-dichlorinated Weinreb amides through a simple work-up procedure

An efficient synthesis of α,β-dichlorinated ketones from α,β-dichlorinated Weinreb amides is described. Quenching with nonaqueous HCl avoided side reactions associated with typical work-up procedures. The amide reacted with various nucleophiles to give the corresponding ketones in high yields. A novel reactivity of the Weinreb amide is also discussed.

Synthesis of Ortho-Functionalized 1,4-Cubanedicarboxylate Derivatives through Photochemical Chlorocarbonylation

The cubane ring has received intense attention as a 3D benzene isostere and scaffold. Mono- and 1,4-disubstituted cubanes are well-described. Here we report a practical procedure for a direct radical-mediated chlorocarbonylation process initially reported by Bashir-Hashemi, to access a range of 2-substituted 1,4-cubanedicarboxylic ester derivatives. A subsequent regioselective ester hydrolysis to give fully differentiated 1,2,4-trisubstituted cubanes is demonstrated.

Synthesis of 1,3-disubstituted bicyclo[1.1.0]butanes via directed bridgehead functionalization

Bicyclo[1.1.0]butanes (BCBs) are increasingly valued as intermediates in ‘strain release’ chemistry for the synthesis of substituted four membered rings and bicyclo[1.1.1]pentanes, with applications including bioconjugation processes. Variation of the BCB bridgehead substituents can be challenging due to the inherent strain of the bicyclic scaffold, often necessitating linear syntheses of specific BCB targets. Here we report the first palladium catalyzed cross-coupling on pre-formed BCBs which enables a ‘late stage’ diversification of the bridgehead position, and the conversion of the resultant products into a range of useful small ring building blocks.

Bicyclo[1.1.0]butanes (BCBs) are valuable precursors to four-membered rings and bicyclo[1.1.1]pentanes, and useful bioconjugation agents. We describe a versatile approach to access 1,3-disubstituted BCBs, which are otherwise challenging to prepare.

A novel vitamin K derived anticoagulant tolerant to genetic variations of vitamin K epoxide reductase

BACKGROUND

Vitamin K antagonists (VKAs), such as warfarin, have remained the cornerstone of oral anticoagulation therapy in the prevention and treatment of thromboembolism for more than half a century. They function by impairing the biosynthesis of vitamin K-dependent (VKD) clotting factors through the inhibition of vitamin K epoxide reductase (VKOR). The challenge of VKAs therapy is their narrow therapeutic index and highly variable dosing requirements, which are partially the result of genetic variations of VKOR.

OBJECTIVES

The goal of this study was to search for an improved VKA that is tolerant to the genetic variations of its target enzyme.

METHODS

A series of vitamin K derivatives with benzyl and related side-chain substitutions at the 3-position of 1,4-naphthoquinone were synthesized. The role of these compounds in VKD carboxylation was evaluated by mammalian cell-based assays and conventional in vitro activity assays.

RESULTS

Our results showed that replacing the phytyl side-chain with a methylene cyclooctatetraene (COT) moiety at the 3-position of vitamin K1 converted it from a substrate to an inhibitor for VKD carboxylation. Strikingly, this COT-vitamin K derivative displayed a similar inhibition potency in warfarin-resistant VKOR mutations whose warfarin resistance varied more than 400-fold. Further characterization of COT-vitamin K for the inhibition of VKD carboxylation suggested that this compound targets multiple enzymes in the vitamin K redox cycle. Importantly, the anticoagulation effect of COT-vitamin K can be rescued with high doses of vitamin K1 .

CONCLUSION

We discovered a vitamin K analogue that functions as a VKA and is tolerant to genetic variations in the target enzyme.

Decagram Synthesis of Dimethyl 1,4-Cubanedicarboxylate Using Continuous-Flow Photochemistry

The highly strained cubane system is of great interest as a scaffold and rigid linker in both pharmaceutical and materials chemistry. A straightforward approach is reported for the scale-up of a [2+2] photocycloaddition step using convenient home-made flow photoreactors to access dimethyl 1,4-cubanedicarboxylate on decagram-scale in 33–40% yield over 8 steps. The process is demonstrated on 3.4 g·h–1 input with 30 minutes residence time, enabling to reduce the process time and to avoid the use of batch photoreactors. Completion of the characterisation of the photocycloadduct and its hydrates is reported.

Nonclassical Phenyl Bioisosteres as Effective Replacements in a Series of Novel Open-Source Antimalarials

The replacement of one chemical motif with another that is broadly similar is a common method in medicinal chemistry to modulate the physical and biological properties of a molecule (i.e., bioisosterism). In recent years, bioisosteres such as cubane and bicyclo[1.1.1]pentane (BCP) have been used as highly effective phenyl mimics. Herein, we show the successful incorporation of a range of phenyl bioisosteres during the open-source optimization of an antimalarial series. Cubane (19) and closo-carborane (23) analogues exhibited improved in vitro potency against Plasmodium falciparum compared to the parent phenyl compound; however, these changes resulted in a reduction in metabolic stability; unusually, enzyme-mediated oxidation was found to take place on the cubane core. A BCP analogue (22) was found to be equipotent to its parent phenyl compound and showed significantly improved metabolic properties. While these results demonstrate the utility of these atypical bioisosteres when used in a medicinal chemistry program, the search to find a suitable bioisostere may well require the preparation of many candidates, in our case, 32 compounds.

Cubane, Bicyclo[1.1.1]pentane and Bicyclo[2.2.2]octane: Impact and Thermal Sensitiveness of Carboxyl-, Hydroxymethyl- and Iodo-substituents

With the burgeoning interest in cage motifs for bioactive molecule discovery, and the recent disclosure of 1,4-cubane-dicarboxylic acid impact sensitivity, more research into the safety profiles of cage scaffolds is required. Therefore, the impact sensitivity and thermal decomposition behavior of judiciously selected starting materials and synthetic intermediates of cubane, bicyclo[1.1.1]pentane (BCP), and bicyclo[2.2.2]octane (BCO) were evaluated via hammer test and sealed cell differential scanning calorimetry, respectively. Iodo-substituted systems were found to be more impact sensitive, whereas hydroxymethyl substitution led to more rapid thermodecomposition. Cubane was more likely to be impact sensitive with these substituents, followed by BCP, whereas all BCOs were unresponsive. The majority of derivatives were placed substantially above Yoshida thresholds-a computational indicator of sensitivity.

Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker

Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker Plasmodium vivax lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of P. vivax over Plasmodium falciparum lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.

Programmable synthesis of multiply arylated cubanes through C-H metalation and arylation

Cubane (C₈H₈), a cubic alkane, has long attracted attention owing to its unique 3D structure. In order to utilize the cubane scaffold widely in science and technology, a powerful method for synthesizing diverse cubane derivatives is required. Herein, we report the synthesis of mono-, di-, tri-, and tetra-arylated cubanes. Directed ortho-metalation with lithium base/alkyl zinc and subsequent palladium-catalyzed arylation enabled C–H metalation and arylation of cubane. This reaction allows the late-stage and regioselective installation of a wide range of aryl groups, realizing the first programmable synthesis of diverse multiply arylated cubanes.

Cubane has attracted attention due to its unique 3D structure. Herein, we report the programmable synthesis of multiply arylated cubanes. The developed reaction allows the late-stage and regioselective installation of aryl groups.

Cubane Electrochemistry: Direct Conversion of Cubane Carboxylic Acids to Alkoxy Cubanes Using the Hofer-Moest Reaction under Flow Conditions

The highly strained cubane system is of great interest as a scaffold and rigid linker in both pharmaceutical and materials chemistry. The first electrochemical functionalisation of cubane by oxidative decarboxylative ether formation (Hofer-Moest reaction) was demonstrated. The mild conditions are compatible with the presence of other oxidisable functional groups, and the use of flow electrochemical conditions allows straightforward upscaling.

1,4-Diazacubane crystal structure rectified as piperazinium

All 21 [n]-azacubanes are proposed by theoreticians to be stable, however, to-date only the synthesis of 1,4-diazacubane has been reported - as a Ni2+ templated Kagome metal organic framework (MOF). Described herein is the structural reassignment of this Kagome MOF on the basis of deducing the precise experimental procedure, and demonstrating that rather than the formation of 1,4-diazacubane, charge is balanced by disordered piperazinium cations across a twelve-fold symmetry site. Furthermore, quantum chemical calculations reveal that 1,4-diazacubane is unlikely to form under the reported conditions due to unfavorable enthalpies for select hypothetical reactions leading to such a product. This significant structure correction upholds the unconquered synthesis status quo of azacubane.