Synthesis of Borylated Carbocycles by [2 + 2]-Cycloadditions and Photo-Ene Reactions.

Saturated bicyclic compounds make up a valuable class of building blocks in the development of agrochemicals and pharmaceuticals. Here, we present the synthesis of borylated bicyclo[2.1.1]hexanes via crossed [2 + 2]-cycloaddition. Due to the presence of the C-B bond, a variety of structures can be easily prepared that are not accessible by other methods. Moreover, a rare photo-ene reaction is also disclosed, allowing for the diastereoselective synthesis of trisubstituted borylated cyclopentanes.

Diversification of Simple Arenes into Complex (Amino)cyclitols.

Highly oxygenated cyclohexanes, including (amino)cyclitols, are featured in natural products possessing a notable range of biological activities. As such, these building blocks are valuable tools for medicinal chemistry. While de novo synthetic strategies have provided access to select compounds, challenges including stereochemical density and complexity have hindered the development of a general approach to (amino)cyclitol structures. This work reports the use of arenophile chemistry to access dearomatized intermediates which are amenable to diverse downstream transformations. Practical guidelines were developed for the synthesis of natural and non-natural (amino)cyclitols from simple arenes through a series of strategic functionalization events.

Reactivity and Selectivity of Azaspirocycles in Radical C-H Functionalization.

Investigations of saturated spirocycles toward selective C-H functionalization reactions are scarce, despite their potential applications. In this work, we uncovered fundamental reactivity and selectivity differences between saturated heterocycles and their spirocyclic analogues using a model radical C-H xanthylation coupled with computational analysis. Ultimately, this study sheds light on the fundamental, understudied radical reactivity of spirocycles, thereby allowing for a pronounced chemical tunability that will prove to be advantageous in the expansion of their chemical space and applications in medicinal chemistry.

Synthesis of 2-Azanorbornanes via Strain-Release Formal Cycloadditions Initiated by Energy Transfer.

Rigid bicycles are becoming more popular in the pharmaceutical industry because they allow for expansion to new and unique chemical spaces. This work describes a new strategy to construct 2-azanorbornanes, which can act as rigid piperidine/pyrrolidine scaffolds with well-defined exit vectors. To achieve the synthesis of 2-azanorbornanes, new strain-release reagent, azahousane, is introduced along with its photosensitized strain-release formal cycloaddition with alkenes. Furthermore, new reactivity between a housane and an imine is disclosed. Both strategies lead to various substituted 2-azanorbornanes with good selectivities.

Introducing covalent warheads on spirocyclic sp2-sp3 fragments by innate C-H functionalization.

Sp2-sp3 fragments play a vital role in fragment-based drug design (FBDD). Strategies to chemically modify them and efficiently access libraries of these compounds have been goals of the highest priority in the last decades. In this work, a series of sp2-sp3 fragments was synthesized and validated for that purpose, based on their measured physical-chemical properties. Selective C-H cyanation and allylation of these fragments was demonstrated by simple heating in presence of an appropriate hydrogen-atom transfer reagent and a radical acceptor. These conditions enabled a streamlined access to covalent fragments in a single step, by direct introduction of the desired covalent binder. Preliminary results on vinylation, as well as late-stage functionalization of a drug analogue were disclosed.

2,5-disubstituted bicyclo[2.1.1]hexanes as rigidified cyclopentane variants.

Identification of rigid counterparts for common flexible scaffolds is crucial to the advancement of medicinal chemistry. Here we showcase a new class of building blocks, 2,5-disubstituted bicyclo[2.1.1]hexanes that can act as rigidified cis-, or trans-1,3-disubstituted cyclopentanes, common motifs in drugs. The scalable synthesis of these structures was enabled through the use of C-H functionalization logic and cycloaddition reactions.

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.

Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios.

The prediction of chemical reaction pathways has been accelerated by the development of novel machine learning architectures based on the deep learning paradigm. In this context, deep neural networks initially designed for language translation have been used to accurately predict a wide range of chemical reactions. Among models suited for the task of language translation, the recently introduced molecular transformer reached impressive performance in terms of forward-synthesis and retrosynthesis predictions. In this study, we first present an analysis of the performance of transformer models for product, reactant, and reagent prediction tasks under different scenarios of data availability and data augmentation. We find that the impact of data augmentation depends on the prediction task and on the metric used to evaluate the model performance. Second, we probe the contribution of different combinations of input formats, tokenization schemes, and embedding strategies to model performance. We find that less stable input settings generally lead to better performance. Lastly, we validate the superiority of round-trip accuracy over simpler evaluation metrics, such as top-k accuracy, using a committee of human experts and show a strong agreement for predictions that pass the round-trip test. This demonstrates the usefulness of more elaborate metrics in complex predictive scenarios and highlights the limitations of direct comparisons to a predefined database, which may include a limited number of chemical reaction pathways.

Preparation of new bicyclo[2.1.1]hexane compact modules: an opening towards novel sp3-rich chemical space.

Among the valuable saturated bicyclic structures incorporated in newly developed bio-active compounds, bicyclo[2.1.1]hexanes are playing an increasingly important role, while being still underexplored from a synthetic accessibility point of view. Here, we disclose an efficient and modular approach toward new 1,2-disubstituted bicyclo[2.1.1]hexane modules. Our strategy is based on the use of photochemistry to access new building blocks via [2 + 2] cycloaddition. The system can readily be derivatized with numerous transformations, opening the gate to sp3-rich new chemical space.

[2]-Ladderanes as isosteres for meta-substituted aromatic rings and rigidified cyclohexanes.

Aromatic ring isosteres and rigidified saturated hydrocarbons are important motifs to enable drug discovery. Herein we disclose [2]-ladderanes as a class of meta-substituted aromatic ring isosteres and rigidified cyclohexanes. A straightforward synthesis of the building blocks is presented along with representative derivatization. Preliminary studies reveal that the [2]-ladderanes offer similar metabolic and physicochemical properties thus establishing this class of molecules as interesting motifs.

Strain-Release [2π + 2σ] Cycloadditions for the Synthesis of Bicyclo[2.1.1]hexanes Initiated by Energy Transfer.

Saturated bicycles are becoming ever more important in the design and development of new pharmaceuticals. Here a new strategy for the synthesis of bicyclo[2.1.1]hexanes is described. These bicycles are significant because they have defined exit vectors, yet many substitution patterns are underexplored as building blocks. The process involves sensitization of a bicyclo[1.1.0]butane followed by cycloaddition with an alkene. The scope and mechanistic details of the method are discussed.

A GAP Replacement, Part 2: Preparation of Poly(3-azidooxetane) via Azidation of Poly(3-tosyloxyoxetane) and Poly(3-mesyloxyoxetane).

Despite the variety of energetic polyoxetane binders, the oxirane-based glycidyl azide polymer (GAP) has largely succeeded in the market due to its advantageous properties. Nevertheless, it suffers from various drawbacks such as non-uniform chain termination, possible chlorine content (flame retardant), and toxic epichlorohydrin required for its synthesis. These problems can be bypassed using the structurally related poly(3-azidooxetane). Unfortunately, it is only accessible in moderate yield by polymerization of 3-azidooxetane. Herein, we describe its synthesis by polymer-analogous transformation using the new polymers poly(3-tosyloxyoxetane) and poly(3-mesyloxyoxetane) as precursors. This results in a significantly increased yield and improved safety as handling of the very sensitive 3-azidooxetane is avoided. The aforementioned prepolymers were prepared using boron trifluoride etherate as well as triisobutylaluminum as catalysts. The latter provides polymers of particularly high molecular weight, and the corresponding poly(3-azidooxetane) species was obtained and studied for the first time. In order to shed light on the applicability of poly(3-azidooxetane) as a GAP substitute, it was thoroughly studied with regard to thermal behavior, energetic performance (EXPLO5), plasticizer compatibility, and curing. Moreover, the aquatic toxicity of all involved monomers was analyzed and compared to epichlorohydrin. Here, poly(3-azidooxetane) turned out as a fully adequate, if not more environmentally benign, substitute.

3,3-Dinitratooxetane - an important leap towards energetic oxygen-rich monomers and polymers.

3-Substituted oxetanes are valuable monomers for modern ring-opening polymerizations. A new solid-state oxidizer, 3,3-dinitratooxetane (C3H4N2O7), which has an oxygen content of 62.2% was synthesized by the addition of N2O5 to oxetan-3-one. Monoclinic single crystals suitable for X-ray diffraction (ρ 1.80 g cm-3) were obtained by recrystallization from dichloromethane. In addition, 3-nitratooxetane was prepared by an improved method and 3-nitrato-3-methyloxetane was synthesized for the first time. Theoretical calculations were computed by the EXPLO5 software and additionally sensitivities towards impact and friction were determined.

Pushing the Frontiers of Accessible Chemical Space to Unleash Design Creativity and Accelerate Drug Discovery.

In highly competitive research environments, the ability to access more complex structural spaces efficiently is a predictor of a company's ability to generate novel IP-protected small molecule candidates with adequate properties, hence filling their development pipelines. SpiroChem is consistently developing new synthetic methodologies and strategies to access complex molecular structure, thereby facilitating and accelerating small molecule drug discovery. Pushing the limits of what are perceived as complex molecular structures allows SpiroChem and its clients to unleash creativity and explore meaningful chemical spaces, which are under-exploited sources of novel active molecules. In this article, we explain how we differentiated ourselves in a globalized R&D environment and we provide several snapshots of how efficient methodologies can generate complex structures, rapidly.

Accelerating fragment-based library generation by coupling high-performance photoreactors with benchtop analysis.

Herein we report a workflow coupling photoredox-nickel dual-catalyzed N-arylation reactions to benchtop analysis for the efficient generation of fragment-based libraries. Technological advances in photoreactor design facilitated reliable and reproducible experimentation. Knowledge on the reactivity under previously reported reaction conditions of spirocyclic and strained heterocyclic building blocks, viewed as chemistry informers, could thus be rapidly accessed, identifying privileged or challenging scaffolds and paving the way for further exploration.

Activating Pyrimidines by Pre-distortion for the General Synthesis of 7-Aza-indazoles from 2-Hydrazonylpyrimidines via Intramolecular Diels-Alder Reactions.

Pyrimidines are almost unreactive partners in Diels-Alder cycloadditions with alkenes and alkynes, and only reactions under drastic conditions have previously been reported. We describe how 2-hydrazonylpyrimidines, easily obtained in two steps from commercially available 2-halopyrimidines, can be exceptionally activated by trifluoroacetylation. This allows a Diels-Alder cycloaddition under very mild reaction conditions, leading to a large diversity of aza-indazoles, a ubiquitous scaffold in medicinal chemistry. This reaction is general and scalable and has an excellent functional group tolerance. A straightforward synthesis of a key intermediate of Bayer's Vericiguat illustrates the potential of this cycloaddition strategy. Quantum mechanical calculations show how the simple N-trifluoroacetylation of 2-hydrazonylpyrimidines distorts the substrate into a transition-state-like geometry that readily undergoes the intramolecular Diels-Alder cycloaddition.

On water N-arylation of oxetanylamines for the preparation of N-aryl-oxetanylamines; potentially useful aryl-amide isosteres.

A Pd cross-coupling approach for the synthesis of N-aryl-oxetanylamines has been developed. This method provides new building blocks potentially useful in medicinal chemistry as amide bioisosteres. The reactions are conducted in water employing the renewable feedstock surfactant TPGS-750-M.

Improving Nonspecific Binding and Solubility: Bicycloalkyl Groups and Cubanes as para-Phenyl Bioisosteres.

Bicycloalkyl groups have been previously described as phenyl group bioisosteres. This article describes the synthesis of new building blocks allowing their introduction into complex molecules, and explores their use as a means to modify the physicochemical properties of drug candidates and improve the quality of imaging agents. In particular, the replacement of an aromatic ring with a bicyclo[1.1.1]pentane-1,3-diyl (BCP) group improves aqueous solubility by at least 50-fold, and markedly decreases nonspecific binding (NSB) as measured by CHI(IAM), the chromatographic hydrophobicity index on immobilized artificial membranes. Structural variations with the bicyclo[2.2.2]octane-1,4-diyl group led to more lipophilic molecules and did not show the same benefits regarding NSB or solubility, whereas substitutions with cubane-1,4-diyl showed improvements for both parameters. These results confirm the potential advantages of both BCP and cubane motifs as bioisosteric replacements for optimizing para-phenyl-substituted molecules.

Oxetanyl peptides: novel peptidomimetic modules for medicinal chemistry.

The synthesis of novel oxetanyl peptides, where the amide bond is replaced by a non-hydrolyzable oxetanylamine fragment, is reported. This new class of pseudo-dipeptides with the same H-bond donor/acceptor pattern found in proteins expands the repertoire of peptidomimetics.