Photochemical Synthesis of 3-Azabicyclo[3.2.0]heptanes: Advanced Building Blocks for Drug Discovery

Synthesis of bicyclo[3.2.0]heptane lactones via a ligand-enabled Pd-catalyzed C(sp3)-H activation cascade

Bicyclo[3.2.0]heptane lactones represent an important scaffold in bioactive molecules. Herein, we report a diastereoselective synthetic disconnection to access bicyclo[3.2.0]heptane lactones from bicyclo[1.1.1]pentane carboxylic acids, which proceeds through palladium-catalyzed C-H activation and C-C cleavage processes. By using two different classes of ligands, MPAA and pyridone-amine, either all-syn arylated bicyclo[3.2.0]heptane lactones or non-arylated ones can be synthesized. The bicyclo[3.2.0]heptane lactone products were converted into multiple substituted cyclobutane, γ-lactone, and oxobicyclo[3.2.0]heptane derivatives to showcase the synthetic versatility of this method.

Photoexcited Copper-Catalyzed Intramolecular [2+2] Cycloaddition To Construct Bicyclo[3.2.0]heptanes

The bicyclo[3.2.0]heptane scaffold is frequently found in a wide range of bioactive molecules and plays a pivotal role in constructing key modules of these compounds. In this study, we present a strategy for the synthesis of bicyclo[3.2.0]heptanes using a copper/BINAP complex to facilitate an intramolecular [2+2] cycloaddition under visible light irradiation. This methodology offers several advantages, including the use of a cost-effective copper catalyst and the ability to achieve high yields (up to 98%) and diastereoselectivity (>20:1 dr). Our approach provides an efficient strategy for constructing the bicyclo[3.2.0]heptane framework.

Metal-free [2+2]-photocycloaddition of unactivated alkenes enabled by continuous flow processing

We report a continuous flow approach generating bicyclic cyclobutanes from unactivated alkenes in a metal-free manner that is inspired by the Kochi-Salomon reaction. A filtered Hg-lamp in combination with a simple flow set-up and acetone as UV light-absorbing co-solvent are crucial for this method thus showcasing attractive features for further exploitations.

4-Azaspiro[2.3]hexane, an Overlooked Piperidine Isostere: Multigram Synthesis and Physicochemical and Structural Evaluation

An expedient approach to the synthesis of 4-azaspiro[2.3]hexane derivatives is described. The synthetic scheme consists of Tebbe olefination of N-Boc-protected 2-azetidinone (including the first use of the deuterated Petasis reagent Cp2Ti(CD3)2 in the building block preparation) and cyclopropanation of the resulting intermediate. The developed protocols allowed for the preparation of target building blocks on a multigram scale (up to 52 g). To illustrate the potential of the obtained 4-azaspiro[2.3]hexane derivatives for isosteric replacements in drug discovery, their physicochemical and structural characterization was performed, i.e., basicity (pKa) and lipophilicity (Log P) measurements, X-ray diffraction studies, and exit vector plot (EVP) analysis.

3-Substituted 6-Azabicyclo[3.1.1]heptanes: Nonclassical Piperidine Isosteres for Drug Discovery

Advanced analogs of piperidine and smaller homologues of tropane─3-substituted 6-azabicyclo[3.1.1]heptanes─were synthesized on a large scale using readily available bulk reagents. The key step of the approach involved the double alkylation reaction of malonate with cis-2,4-bis(mesyloxymethyl)azetidine-1-carboxylate, in turn easily prepared on up to 1 kg scale. After hydrolysis, N-Boc-6-azabicyclo[3.1.1]heptane-3,3-dicarboxylic acid was obtained (up to 400 g in a single run), which was used as a common intermediate for the preparation of all the title building blocks. In particular, Pb(OAc)4-mediated oxidative decarboxylation of this intermediate gave 2,6-methanopiperidone derivative (up to 400 g scale), while monodecarboxylation gave N-Boc-6-azabicyclo[3.1.1]heptane-3-carboxylic acids as an easily separatable mixture of cis and trans diastereomers (up to 100 g scale). Further functional group transformations gave diastereopure cis- and trans-N-Boc-monoprotected diamines and amino alcohols. Molecular structure analysis using exit vector parameters (EVP) revealed that cis isomers of 3-substituted 6-azabicyclo[3.1.1]heptanes are three-dimensional analogs of common 1,4-disubstituted piperidine chair conformer, whereas trans isomers can be considered as unusual "boat" piperidines.

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.

Aqueous Amine-Tolerant [2+2] Photocycloadditions of Unactivated Olefins

The Kochi-Salomon reaction is the only photochemical [2+2] cycloaddition capable of combining two electronically unactivated olefins into a cyclobutane. Yet, the reaction has remained largely unexplored and suffers many drawbacks, most notably an intolerance to Lewis/Brønsted basic amines and amides. Since these groups are ubiquitous in biologically active pharmaceuticals, an amine-tolerant Kochi-Salomon reaction would greatly facilitate rapid exploration of novel drug scaffolds. Herein, we disclose a transformation that is run in water with the most widely available Cu(II) salts and mineral acids. Furthermore, we apply this methodology to synthesize a variety of amine-containing cyclobutanes, including known and novel pharmacological analogues.

Large-Scale Synthesis and Modifications of Bicyclo[1.1.1]pentane-1,3-dicarboxylic Acid (BCP)

In flow photochemical addition of propellane to diacetyl allowed construction of the bicyclo[1.1.1]pentane (BCP) core in a 1 kg scale within 1 day. Haloform reaction of the formed diketone in batch afforded bicyclo[1.1.1]pentane-1,3-dicarboxylic acid in a multigram amount. Representative gram scale transformations of the diacid were also performed to obtain various BCP-containing building blocks—alcohols, acids, amines, trifluoroborates, amino acids, etc.—for medicinal chemistry.

Bicyclic Pyrrolidines for Medicinal Chemistry via [3 + 2]-Cycloaddition

A general approach to bicyclic fused pyrrolidines via [3 + 2]-cycloaddition between nonstabilized azomethyne ylide and endocyclic electron-deficient alkenes was elaborated. "Push-pull" alkenes and CF₃-alkenes did not react with the azomethyne ylide under the previously reported conditions, and we developed a superior protocol (LiF, 140 °C, no solvent). Among obtained products were medchem-relevant bicyclic sulfones, monofluoro-, difluoro-, and trifluoromethyl-substituted pyrrolidines. This approach not only allowed preparation of novel molecules but also significantly simplified synthesis of the existing ones (e.g., sofinicline).

A catalytic asymmetric cross-coupling approach to the synthesis of cyclobutanes

Stereodefined four-membered rings are common motifs in bioactive molecules and versatile intermediates in organic synthesis. However, the synthesis of complex, chiral cyclobutanes is a largely unsolved problem and there is a need for general and modular synthetic methods. Here we report a series of asymmetric cross-coupling reactions between cyclobutenes and arylboronic acids which are initiated by Rh-catalysed asymmetric carbometallation. After the initial carborhodation, Rh-cyclobutyl intermediates undergo chain-walking or C-H insertion so that overall a variety of additions such as reductive Heck reactions, 1,5-addition and homoallylic substitution are observed. The synthetic applicability of these highly stereoselective transformations is demonstrated in the concise syntheses of the drug candidates Belaperidone and PF-04862853. We anticipate this approach will be widely adopted by synthetic and medicinal chemists. While the carbometallation approach reported here is exemplified with Rh and arylboronic acids, it is likely to be applicable to other metals and nucleophiles.

Photocatalyzed Intramolecular [2+2] Cycloaddition of N-Alkyl-N-(2-(1-arylvinyl)aryl)cinnamamides

N-Alkyl-N-(2-(1-arylvinyl)aryl)cinnamamides are converted into natural product inspired scaffolds via iridium photocatalyzed intramolecular [2+2] photocycloaddition. The protocol has a broad substrate scope, whilst operating under mild reaction conditions. Tethering four components forming a trisubstituted cyclobutane core builds rapidly high molecular complexity. Our approach allows the design and synthesis of a variety of tetrahydrocyclobuta[c]quinolin-3(1H)-ones, in yields ranging between 20-99 %, and with excellent regio- and diastereoselectivity. Moreover, it was demonstrated that the intramolecular [2+2]-cycloaddition of 1,7-enynes-after fragmentation of the cyclobutane ring-leads to enyne-metathesis-like products.

Bicyclic Piperidines via [2 + 2] Photocycloaddition

A synthetic strategy to fused bicyclic piperidines-building blocks for medicinal chemistry-is developed. The key step was an intramolecular [2 + 2]-photocyclization. The photochemical step was performed on a gram scale. Crystallographic analysis of the obtained compounds revealed that they occupy a novel chemical space and can be considered as elongated analogues of 3-substituted piperidines.

Rational Design of Triplet Sensitizers for the Transfer of Excited State Photochemistry from UV to Visible

Time Dependent Density Functional Theory has been used to assist the design and synthesis of a series thioxanthone triplet sensitizers. Calculated energies of the triplet excited state (E_T) informed both the type and position of auxochromes placed on the thioxanthone core, enabling fine-tuning of the UV-vis absorptions and associated triplet energies. The calculated results were highly consistent with experimental observation in both the order of the λ_max and E_T values. The synthesized compounds were then evaluated for their efficacies as triplet sensitizers in a variety of UV and visible light preparative photochemical reactions. The results of this study exceeded expectations; in particular [2 + 2] cycloaddition chemistry that had previously been sensitized in the UV was found to undergo cycloaddition at 455 nm (blue) with a 2- to 9-fold increase in productivity (g/h) relative to input power. This study demonstrates the ability of powerful modern computational methods to aid in the design of successful and productive triplet sensitized photochemical reactions.

Saturated Bioisosteres of ortho-Substituted Benzenes

Saturated bioisosteres of ortho-disubstituted benzenes (bicyclo[2.1.1]hexanes) were synthesized, characterized and validated. These cores were incorporated into the bioactive compounds Valsartan, Boskalid and Fluxapyroxad instead of the benzene ring. The saturated analogues showed a similar level of antifungal activity compared to that of Boskalid and Fluxapyroxad.

C(sp3)-H arylation to construct all-syn cyclobutane-based heterobicyclic systems: a novel fragment collection

All-syn fused cyclobutanes remain an elusive chemotype and thus present an interesting synthetic challenge. Herein, we report the successful application of Pd-catalysed C(sp3)-H arylation of cyclobutane compounds to generate all-syn heterobicyclic fragments using an innovative 'inside-out' approach. Through this strategy we generate a virtual collection of 90 fragments, which we demonstrate to have enhanced three-dimensionality and superior fragment-like properties compared to existing collections.

Photochemical [2 + 2] Cycloaddition of Alkenyl Boronic Derivatives: An Entry into 3-Azabicyclo[3.2.0]heptane Scaffold

The synthesis of 3-azabicyclo[3.2.0]heptyl boropinacolates and trifluoroborates via the [2 + 2] photocycloaddition of the corresponding alkenyl boronic derivatives and maleimides or maleic anhydride is described. Optimization of the reaction conditions (i.e., wavelength, concentration of the reagents, photosensitizer) was carried out, and the scope and limitations of the method were studied. Alkenyl boronic acid pinacolates were found to be more suitable for the [2 + 2] cycloaddition, providing better reaction outcomes compared to the trifluoroborates. The utility of this approach was shown by the preparation of bi- and trifunctional building blocks (21 examples), which could be easily synthesized on up to 60 g scale. These cycloadducts provide a convenient entry into the 3-azabicyclo[3.2.0]heptane scaffold through the C-C coupling or oxidative deborylation reactions.

Water-Soluble Non-Classical Benzene Mimetics

A new generation of saturated benzene mimetics, 2-oxabicyclo[2.1.1]hexanes, was developed. These compounds were designed as analogues of bicyclo[1.1.1]pentane with an improved water solubility. Crystallographic analysis of 2-oxabicyclo[2.1.1]hexanes revealed that they occupy a novel chemical space, but, at the same time, resemble the motif of meta-disubstituted benzenes.

Building the Housane: Diastereoselective Synthesis and Characterization of Bicyclo[2.1.0]pentane Carboxylic Acids

An approach to 1,3-disubstitued bicyclo[2.1.0]pentane (housane) derivatives was developed. The method relied on lithium bis(trimethylsilyl)amide-mediated intramolecular cyclization of trisubstitued cyclopentane carboxylates bearing a leaving group (at the C-4 position) and an additional substituent (at the C-3 atom), in turn synthesized from cyclopent-3-ene carboxylate. The synthetic sequence allowed for the preparation of both cis- and trans-1,3-disubstituted housane-1-carboxylic acids in diastereoselective manner on up to 80 g scale. In particular, bicyclic γ-amino acids-γ-aminobutyric acid analogues-were synthesized. It was shown that the bicyclo[2.1.0]pentane did not significantly affect pK_a of the corresponding derivatives and slightly increased their hydrophilicity (by 0.07-0.25 Log P units) as compared to cyclopentane. X-ray diffraction studies showed that cis- and trans-1,3-disubstituted housanes can be considered as flattened analogues of the corresponding cyclopentane derivatives with fixed envelope conformation of the five-membered ring.

Synthesis of Cyclobutane-Fused Tetracyclic Scaffolds via Visible-Light Photocatalysis for Building Molecular Complexity

We describe the synthesis through visible-light photocatalysis of novel functionalized tetracyclic scaffolds that incorporate a fused azabicyclo[3.2.0]heptan-2-one motif, which are structurally interesting cores with potential in natural product synthesis and drug discovery. The synthetic approach involves an intramolecular [2 + 2] cycloaddition with concomitant dearomatization of the heterocycle via an energy transfer process promoted by an iridium-based photosensitizer, to build a complex molecular architecture with at least three stereogenic centers from relatively simple, achiral precursors. These fused azabicyclo[3.2.0]heptan-2-one-based tetracycles were obtained in high yield (generally >99%) and with excellent diastereoselectivity (>99:1). The late-stage derivatization of a bromine-substituted, tetracyclic indoline derivative with alkyl groups, employing a mild Negishi C-C bond forming protocol as a means of increasing structural diversity, provides additional modularity that will enable the delivery of valuable building blocks for medicinal chemistry. Density functional theory calculations were used to compute the T₁-S₀ free energy gap of the olefin-tethered precursors and also to predict their reactivities based on triplet state energy transfer and transition state energy feasibility.

Escaping from Flatland: [2 + 2] Photocycloaddition; Conformationally Constrained sp3-rich Scaffolds for Lead Generation

Pressure on researchers to deliver new medicines to the patient continues to grow. Attrition rates in the research and development process present a significant challenge to the viability of the current model of drug discovery. Analysis shows that increasing the three-dimensionality of potential drug candidates decreases the risk of attrition, and it is for this reason many workers have taken a new look at the power of photochemistry, in particular photocycloadditions, as a means to generate novel sp³-rich scaffolds for use in drug discovery programs. The viability of carrying out photochemical reactions on scale is also being addressed by the introduction of new technical developments.

Far Away from Flatland. Synthesis and Molecular Structure of Dihetera[3.3.n]propellanes and Trihetera[3.3.n]propellanes: Advanced Analogues of Morpholine/Piperazine

An approach to di- and trihetera[3.3.n]propellanes (n = 2-4 ), advanced morpholine and piperazine analogues, is developed. The key step of the reaction sequence included a [3 + 2] cycloaddition reaction of unsaturated vicinal dicarboxylic acid derivatives and in situ generated azomethine ylide resulting in the formation of the pyrrolidine ring. One more heteroaliphatic ring (i.e., pyrrolidine or tetrahydrofuran) was annelated by nucleophilic cyclization of the appropriate 1,4-dielectrophilic intermediates. There were 11 examples of the title products obtained in 3-5 steps on a multigram scale with 10-72% overall yields. Additionally, molecular structures of homologous dihetera[3.3.n]propellanes, analogues of morpholine, were obtained from X-ray diffraction studies and analyzed using exit vector plots (EVPs). It was shown that the scaffolds obtained are somewhat larger as compared to the parent morpholine and bicyclic 3-oxa-7-azabicyclo[3.3.0]octane. Moreover, despite very similar chemical structures, they provide a very distinct spatial position of heteroatoms, which is clearly seen from the conformation adopted by a formal eight-membered ring including both N and O atoms (i.e., crown, boat-chair, twist chair-chair, and boat-boat for the oxaza[3.3.2]-, -[3.3.3]-, -[4.3.3]propellanes, and 3-oxa-7-azabicyclo[3.3.0]octane, respectively).

Photochemical In-Flow Synthesis of 2,4-Methanopyrrolidines: Pyrrolidine Analogues with Improved Water Solubility and Reduced Lipophilicity

A practical synthesis of 2,4-methanopyrrolidines was elaborated. The key synthetic step was an intramolecular photochemical [2 + 2]-cycloaddition of an acrylic acid derivative in flow. In spite of a higher molecular weight, 2,4-methanopyrrolidines were shown to have higher solubility in water and lower lipophilicity than pyrrolidines, important characteristics of bioactive molecules in drug design.

Synthesis of Multifunctional Spirocyclic Azetidines and Their Application in Drug Discovery

The synthesis of multifunctional spirocycles was achieved from common cyclic carboxylic acids (cyclobutane carboxylate, cyclopentane carboxylate, l-proline, etc.). The whole sequence included only two chemical steps-synthesis of azetidinones, and reduction into azetidines. The obtained spirocyclic amino acids were incorporated into a structure of the known anesthetic drug Bupivacaine. The obtained analogues were more active and less toxic than the original drug. We believe that this discovery will lead to a wide use of spirocyclic building blocks in drug discovery in the near future.

Synthesis of CHF2-substituted 3-azabicyclo[3.1.0]hexanes by photochemical decomposition of CHF2-pyrazolines

A practical synthesis of CHF2-substituted 3-azabicyclo[3.1.0]hexanes was developed for the first time. The key step was photochemical decomposition of CHF2-substituted pyrazolines. This protocol has the advantages of simple operation, and mild conditions, as well as excellent functional group tolerance, giving the desired products in moderate to excellent yields.

Following Ramachandran 2: exit vector plot (EVP) analysis of disubstituted saturated rings

EVP analysis of common saturated rings revealed five regions (α–ε); only part of them corresponds to 3D molecular structures.

The unequivocal preponderance of biocomputation in clinical virology

Bioinformatics and computer based data simulation and modeling are captivating biological research, delivering great results already and promising to deliver more. As biological research is a complex, intricate, diverse field, any available support is gladly taken. With recent outbreaks and epidemics, pathogens are a constant threat to the global economy and security. Virus related plagues are somehow the most difficult to handle. Biocomputation has provided appreciable help in resolving clinical virology related issues. This review, for the first time, surveys the current status of the role of computation in virus related research. Advances made in the fields of clinical virology, antiviral drug design, viral immunology and viral oncology, through input from biocomputation, have been discussed. The amount of progress made and the software platforms available are consolidated in this review. The limitations of computation based methods are presented. Finally, the challenges facing the future of biocomputation in clinical virology are speculated upon.

Biocomputation in clinical virology.

Synthesis of Spirocyclic Pyrrolidines: Advanced Building Blocks for Drug Discovery

In the context of drug discovery, novel spirocyclic pyrrolidines have been synthesized in two steps from common three- to seven-membered-ring (hetero)alicyclic ketones. The key transformation is a reaction between an electron-deficient exocyclic alkene and an in situ generated N-benzyl azomethine ylide. The developed method has been used to synthesize the central diamine core of the known antibacterial agents Sitafloxacin and Olamufloxacin.