Rings in Clinical Trials and Drugs: Present and Future

The chiral 5,6-cyclohexane-fused uracil ring-system: A molecular platform with promising activity against SARS-CoV-2

The recurrent global exposure to highly challenging viral epidemics, and the still limited spectrum of effective pharmacological options step on the accelerator towards the development of new antiviral medicines. In this work we explored the anti-SARS-CoV-2 potential of a recently launched chiral ring system based on the uracil scaffold fused to carbocycle rings. The asymmetric synthesis of two generations of chiral uracil-based compounds (overall 31 different products), and their in vitro cytotoxicity and antiviral screening against wild-type SARS-CoV-2 in U87.ACE cells allowed us to identify seven non-cytotoxic enantioenriched derivatives exhibiting in vitro EC50 in the 6-37 μM range. Among these compounds, bicyclic uracil 10 showed the best antiviral potency against SARS-CoV-2 (EC50 20A.EU2 = 7.41 μM and EC50 Omicron = 19.4 μM), combined with a favourable selectivity index. Additionally, it exhibited single-digit micromolar inhibition of the isolated SARS-CoV-2 RNA-dependent RNA polymerase (IC50 = 2.1 μM). Starting from a reported cryo-EM structure of RdRp, docking and molecular dynamics simulations were performed to rationalize possible binding modes of the active compounds. Interestingly, no inhibition of viral replication in cells was observed against a wide spectrum of human viruses, while some derivatives, and especially hit compound 10, exhibited specific low micromolar antiviral effect against β-coronavirus OC43. Collectively, these data indicate that this novel uracil-based ring system represents a valid starting point for further development of a new class of RdRp inhibitors to treat SARS-CoV-2 and, potentially, other β-coronavirus infections.

Cheminformatic Analysis of Core-Atom Transformations in Pharmaceutically Relevant Heteroaromatics

Heteroaromatics are the basis for many pharmaceuticals. The ability to modify these structures through selective core-atom transformations, or "skeletal edits", can dramatically expand the landscape for drug discovery and development. However, despite the importance of core-atom modifications, the quantitative impact of such transformations on accessible chemical space remains undefined. Here, we report a cheminformatic platform to analyze which skeletal edits would most increase access to novel chemical space. This study underscores the significance of emerging single and multiple core-atom transformations of heteroaromatics in enhancing chemical diversity, for example, at a late-stage of a drug discovery campaign. Our findings provide a quantitative framework for prioritizing core-atom modifications in heteroaromatic structural motifs, calling for the development of new methods to achieve these types of transformations.

Defluorinative Diazolation-Cyclization Relay for Synthesis of Furan-Bridged Triheterocycles and Colorimetric Sensor Application

Polyaromatics, as the assembly of diverse cyclic π-systems, exhibit unique physicochemical properties when compared to their individual constituents. In this study, we developed a strategic connection of two azacycles via a furan bridge through a defluorinative diazolation-cyclization reaction of trifluoromethyl enones and N-heterocycles. A range of modular 2,4-furan-bridged triheterocycles (FBTHs), featuring a C3-trifluoromethyl group, was synthesized with broad substrate scope and good regioselectivity under transition metal-free conditions. This three-component protocol was achieved through successive C(sp3)-F bond functionalization of one trifluoromethyl group, which is recognized for its stability and durability. Moreover, the synthetically useful functionalities such as bromide and formyl group could be easily installed on the resulting products, and the imidazole-containing FBTH could serve as a valuable ligand in the preparation of an advanced colorimetric sensor, thereby underscoring their potential applications.

Novel spiroisatin-pyranopyrazole hybrids as anticancer agents with TrkC inhibitory potential

Cancer still represents a global health concern due to its high mortality and morbidity rates. Isatin-and pyrazole-based compounds have recently garnered interest as novel anticancer agents. A series of 15 novel spiroisatin pyranopyrazole derivatives were synthesized. Anticancer potential of synthesized agents against EBC-1, HT-29, A549, and AsPC-1 cell lines, representing cancers of the lung, colon, and pancreas, were evaluated using the MTT assay. The possible molecular mechanism contributing to antiproliferative activities of the most potent compounds was further investigated in silico by using SuperPred web server, a ligand-based tool. Docking and molecular dynamics (MD) simulation studies were carried out to investigate the binding affinity and key interactions of the agents with their predicted target. Among the tested compounds, four cyanide-containing derivatives 6c, 6d, 6f, and 6g with bromobenzyl, chlorobenzyl, p-tButyl benzyl and methylbenzyl moieties on the isatin ring, respectively, displayed the highest antiproliferative effects against all four cell lines. These compounds were particularly effective against EBC-1, and HT-29 cells with IC50 values of 3.3-7.1 and 7.3-10.2 μΜ, respectively, while relatively sparing non-cancer cells. The obtained target prediction results suggested that the growth inhibitory activity of the analyzed analogues could be related to tropomyosin receptor kinase C (TrkC) inhibition. The outcomes of molecular docking and MD simulation demonstrated that the most active agents may interact closely with the active site of the suggested target, further confirming target prediction findings. The findings of this study suggest the potential of spiroisatin pyranopyrazole analogues for further exploration as novel targeted anticancer agents.

Mechanistic insights into the regiodivergent insertion of bicyclo[1.1.0]butanes towards carbocycle-tethered N-heteroarenes

Ring scaffolds constitute important sub-structures in nature and across the chemical industries. However, their straight-forward introduction into a target molecule or cross-linkage between cyclic motifs of choice comprise major challenges for methodology development. Herein, the interconnection of two prominent representatives of the 2D and 3D cyclic chemical space-namely N-heteroarenes and unsaturated carbocycles-in the form of hybrid cyclobutane-tethered N-heteroarenes is targeted. The diastereoselective introduction of decorated cyclobutanes is promoted by the insertion of strained bicyclo[1.1.0]butanes (BCBs) into the C-S bond of C2-thioether aza-arenes. In-depth density functional theory (DFT) studies provide insights on the key factors governing the unexpected regiodivergent insertion outcomes. A broad scope of mono- and bicyclic aza-arenes along with mono- and disubstituted BCBs are shown to be competent. Detailed mechanistic studies support an oxidative activation of the N-heteroarenes.

Development of Chiral-At-Ruthenium Mesoionic Carbene Catalysts

Building on our previously established chiral-at-metal approach, in which the overall chirality of the transition metal catalyst is solely determined by a stereogenic metal center, we here present a new addition to the family of C2-symmetric chiral-at-ruthenium catalysts. These are C2-symmetric chiral ruthenium complexes featuring strongly σ-donating 1,2,3-triazol-5-ylidene mesoionic carbene (MIC) ligands. The complexes demonstrate excellent catalytic activity and enantioselectivity in a nitrene-mediated ring-closing C(sp3)-H amination of an aliphatic azide, leading to the formation of an N-Boc-protected chiral pyrrolidine. This study highlights the potential of this new class of chiral mesoionic carbene ruthenium complexes to further enhance or modify the reactivity of ruthenium-based chiral-at-metal catalysts.

Are activation barriers of 50-70 kcal mol-1 accessible for transformations in organic synthesis in solution?

High-temperature organic chemistry represents a transformative approach for accessing reaction pathways previously considered unattainable under conventional conditions. This study focuses on a high-temperature synthesis as a powerful method for performing solution-phase organic reactions at temperatures up to 500 °C. Using the isomerization of N-substituted pyrazoles as a model reaction, we demonstrate the ability to overcome activation energy barriers of 50-70 kcal mol-1, achieving product yields up to 50% within reaction times as short as five minutes. The methodology is environmentally friendly, leveraging standard glass capillaries and p-xylene as a solvent. The significance of high-temperature synthesis lies in its simplicity, efficiency, and ability to address the limitations of traditional methods in solution chemistry. Kinetic studies and DFT calculations validate the experimental findings and provide insights into the reaction mechanism. The method holds broad appeal due to its potential to access diverse compounds relevant to pharmaceuticals, agrochemicals, and materials science. By expanding the scope of accessible reactions, this exploration of experimental possibilities opens a new frontier in synthetic chemistry, enabling the exploration of previously inaccessible transformations. This study establishes a new direction for further innovations in organic synthesis, fostering advancements in both fundamental research and practical applications.

Diverse Synthesis of Arene-Fused [n.1.1]-Bridged Molecules via Catalytic Cycloaddition and Rearrangement Reactions

Although great advancement has been made in synthesis of 3D bridged bicyclic[n.1.1]-bioisosteres, facile construction of 2D/3D merged molecules incorporating bridged rings, as novel chemical space in drug discovery, remains a significant challenge. Herein a collective, selective, and diversity-oriented approach for up to 6 types of 2D/3D polycyclic scaffolds featuring bicyclo[n.1.1] substructure is reported. A boronyl radical-catalyzed [2σ+2π] cycloaddition between bicyclo[1.1.0]butanes and ortho-quinone methides afforded spirocyclic compounds containing a bicyclo[2.1.1]hexanes unit, which were used as intermediates for synthesis of three types of 2D/3D scaffolds via judiciously controlled Lewis acid-catalyzed rearrangements. The reaction and rearrangement of para-quinone methides worked analogously and provided another two polycyclic scaffolds.

Highly Sensitive and Interference-Free Detection of Multiple Drug Molecules in Serum Using Dual-Modified SERS Substrates Combined with AI Algorithm Analysis

Surface-enhanced Raman spectroscopy (SERS) technology has shown broad potential in drug concentration detection, but its application in blood drug monitoring faces significant challenges. The primary difficulty lies in overcoming the interference caused by various biomolecules present in serum, which can severely obscure the SERS signals of target drug molecules. Traditional enhancement substrates are often limited to detecting single drugs and are prone to interference, making the label-free detection of multiple drugs particularly challenging. To address these issues, we developed a novel SERS substrate based on Au@AgNRs, which undergoes a two-step modification to produce Au@AgDBCNRs. This innovative substrate provides exceptional signal amplification, simultaneously allowing the sensitive detection of multiple drug molecules. Moreover, our method eliminates the need for serum deproteinization, enabling the direct detection of drugs in serum while effectively mitigating interference from blood components. The cetyltrimethylammonium bromide coating on Au@AgDBCNRs is an internal standard for drug quantification without additional standards. The platform significantly improves detection accuracy and efficiency by automatically integrating artificial intelligence to recognize and analyze Raman spectral features. This novel SERS platform provides a new idea for therapeutic drug monitoring and is expected to provide rapid, accurate, and cost-effective drug detection in the clinical environment, which has great potential in improving patient care and optimizing drug dosage strategies.

Physicochemical and Biological Evaluation of gem-Difluorinated Saturated Oxygen Heterocycles as Bioisosteres for Drug Discovery

A comprehensive study on the physicochemical properties of gem-fluorinated O-heterocyclic substituents is reported. Systematic additive effects of introducing O- and gem-CF2 group introduction on acidic properties (pKa) of the corresponding carboxylic acids/protonated primary amines were demonstrated. The impact of the O/CF2 moieties on lipophilicity (LogP) was found to be complex; significant mutual influence of the corresponding polar moieties governed the compound's overall properties in this case. Biological evaluation of MAPK kinase inhibitors incorporating the title substituents demonstrated their utility as promising fragments for bioisosteric replacements in drug discovery campaigns.

"Angular" Spirocyclic Azetidines: Synthesis, Characterization, and Evaluation in Drug Discovery

The previously neglected "angular" spirocyclic azetidines have been synthesized, characterized, and validated in drug discovery. We have shown that these compounds could act as bioisosteres for common saturated six-membered heterocycles. Their incorporation into the structure of the anticancer drug Sonidegib (instead of morpholine), and Danofloxacine (instead of piperazine) provided novel patent-free analogs with similar physicochemical properties and high activity.

Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage

A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.

Discovery of novel tris-1,2,3-triazole-based hybrids as VEGFR2 inhibitors with potent anti-proliferative and cytotoxicity through apoptosis induction

The discovery of novel anti-cancer drugs motivated us to synthesize a new series of triple 1,2,3-triazole-based arm scaffolds featuring distinct un functionalized alkyl and/or aryl side chains with possible anti-cancer action using the click chemistry approach under both conventional and green microwave irradiation (MWI) methods. The Cu(I) catalyzed cycloaddition reaction of targeted tris-alkyne with un functionalized aliphatic and aromatic azides has been adopted as an efficient approach for synthesizing the desired click adducts. Microwave irradiation improved the synthetic processes, resulting in higher yields and faster reaction times. Spectroscopic techniques (FT-IR, 1H, 13C NMR andCHN analysis) were used for the elucidation of the resulting click structures. The newly synthesized tris-1,2,3-triazoles exhibited promising cytotoxicity, particularly compounds 26 and 28, with IC50 values of 22.18 µM and 20.3 µM against A549 and CaCo-2 cells, respectively. While they had IC50 values of 23.06 µM and 21.91 µM against T-47D and CaCo-2 cells, respectively. Both compounds exhibited promising anti-proliferative activity through the wound healing assay. Additionally, both compounds induced total apoptotic cell death by 68.3 % and 58.5 %, respectively, compared to untreated cells (7.7 %). Furthermore, they induced necrotic cell death by 1.4 % and 10.5 %, respectively, compared to 0.1 % in the untreated cells. For the molecular target, compounds 26 and 28 exhibited potent VEGFR2 inhibition with IC50 values of 35.5 nM and 27.8 nM, respectively, and this was highlighted through the molecular docking findings. Tris-1,2,3-triazoles (26 and 28) exhibited promising cytotoxicity and anti-proliferative against T-47D breast cancer cells through apoptosis and VEGFR2 inhibition using both enzyme kit and western blotting protein expression assays. Molecular docking study highlighted the binding affinity of tested compounds towards the VEGFR2 protein. Accordingly, tris-1,2,3-triazoles (26 and 28) can be further developed as more potent anti-cancer agents.

Analyzing Oxygen Atom Distribution in FDA-Approved Drugs to Enhance Drug Discovery Strategies

Despite advancements in molecular design rules and understanding biochemical processes, the field of drug design and discovery seeks to minimize the number and duration of synthesis-testing cycles to convert lead compounds into drug candidates. A promising strategy involves gaining insightful understanding of key heteroatoms such as oxygen and nitrogen. This work presents a comprehensive analysis of oxygen atoms in approved drugs, aiming to streamline drug design and discovery efforts. The study examines the frequency, distribution, prevalence, and diversity of oxygen atoms in a dataset of 2049 small molecules approved by the FDA and other agencies. The analysis focuses on various types of oxygen atoms, including sp3, sp2-hybridized, ring, and nonring. In general, existence of sp3-O slightly outperforms sp2-O, which is associated with balancing various factors such as flexibility, solubility, stability, and pharmacokinetics, in addition to activity and selectivity. In approved drugs, majority of oxygen atoms are present within 4 Å from the COM of the molecule. This analysis offers valuable understanding of oxygen distribution, which could be used during the multiparameter optimization process, facilitating the transformation of a hit/lead compound into a potential drug candidate.

Energy-Transfer Enabled 1,4-Aryl Migration

Functional group translocation is undoubtedly a pivotal synthetic transformation in organic chemistry. Numerous types of reactions involving radical 1,2-aryl or 1,4-aryl migration via electron transfer mechanism have been extensively investigated. Nevertheless, energy-transfer enabled 1,4-arylation remains unknown. Herein we disclose that an unprecedented di-π-ethane rearrangement featuring 1,4-aryl migration facilitated by energy transfer catalysis under visible light conditions. The newly developed mild protocol exhibits tolerance towards diverse functional groups and enables the migration of a multitude of aromatic rings, encompassing both electron-withdrawing and electron-rich functional groups. The open-shell strategy has also found successful application in the modification of several drugs. Large-scale experiments, continuous-flow experiment, and versatile manipulation of products have demonstrated the robustness and potential utility of this synthetic method. Preliminary mechanistic studies have supported the involvement of radical species in this di-π-ethane rearrangement and have also provided evidence for the energy transfer mechanism.

Saturated F2-Rings from Alkenes

A general method to convert simple exocyclic alkenes into saturated F2-rings has been developed. The reaction involves reagent C6F5I(OAc)2. The reaction efficiently works on the mg-, g-, and even multigram scale.

High-Throughput Screening of More Than 30,000 Compounds for Anthelmintics against Gastrointestinal Nematode Parasites

Gastrointestinal nematodes (GINs) are among the most common parasites of humans, livestock, and companion animals. GIN parasites infect 1-2 billion people worldwide, significantly impacting hundreds of millions of children, pregnant women, and adult workers, thereby perpetuating poverty. Two benzimidazoles with suboptimal efficacy are currently used to treat GINs in humans as part of mass drug administrations, with many instances of lower-than-expected or poor efficacy and possible resistance. Thus, new anthelmintics are urgently needed. However, screening methods for new anthelmintics using human GINs typically have low throughput. Here, using our novel screening pipeline that starts with human hookworms, we screened 30,238 unique small molecules from a wide range of compound libraries, including ones with generic diversity, repurposed drugs, natural derivatives, known mechanisms of action, as well as multiple target-focused libraries (e.g., targeting kinases, GPCRs, and neuronal proteins). We identified 55 compounds with broad-spectrum activity against adult stages of two evolutionary divergent GINs, hookworms (Ancylostoma ceylanicum) and whipworms (Trichuris muris). Based on known databases, the targets of these 55 compounds were predicted in nematode parasites. One novel scaffold from the diversity set library, F0317-0202, showed good activity (high motility inhibition) against both GINs. To better understand this novel scaffold's structure-activity relationships (SAR), we screened 28 analogs and created SAR models highlighting chemical and functional groups required for broad-spectrum activity. These studies validate our new and efficient screening pipeline at the level of tens of thousands of compounds and provide an important set of new GIN-active compounds for developing novel and broadly active anthelmintics.

Multicomponent reactions (MCRs) yielding medicinally relevant rings: a recent update and chemical space analysis of the scaffolds

In this review we have compiled multicomponent reactions (MCRs) that produce cyclic structures. We have covered articles reported since 2019 to showcase the recent advances in this area. In contrast to other available reviews on this topic, we focus specifically on MCRs with strong prospects in medicinal chemistry. Consequently, the reactions operating in a single-pot and yielding novel rings or new substitution patterns under mild conditions are highlighted. Moreover, MCRs that do not require special reagents or catalysts and yield diverse products from commercially available building blocks are reviewed. The synthetic schemes, substrate scope, and other key aspects such as regio- and stereoselectivity are discussed for each MCR. Using cheminformatic tools, we have also attempted to characterize the chemical space of the scaffolds obtained from these MCRs. We show that the MCR scaffolds are novel, more complex, and globular in shape compared to the approved drugs and clinical candidates. Thus, our review represents a step towards identifying and characterizing the novel ring space that can be accessed efficiently through MCRs in a short timeframe.

Mechanochemical Radical Transformations in Organic Synthesis

Organic synthesis has historically relied on solution-phase, polar transformations to forge new bonds. However, this paradigm is evolving, propelled by the rapid evolution of radical chemistry. Additionally, organic synthesis is witnessing a simultaneous resurgence in mechanochemistry, the formation of new bonds in the solid-state, further contributing to this shift in the status quo. The aforementioned advances in radical chemistry have predominantly occurred in the solution phase, while the majority of mechanochemical synthesis advances feature polar transformations. Herein, we discuss a rapidly advancing area of organic synthesis: mechanochemical radical reactions. Solid-state radical reactions offer improved green chemistry metrics, better reaction outcomes, and access to intermediates and products that are difficult or impossible to reach in solution. This review explores these reactions in the context of small molecule synthesis, from early findings to the current state-of-the-art, underscoring the pivotal role solid-state radical reactions are likely to play in advancing sustainable chemical synthesis.

Photochemical permutation of thiazoles, isothiazoles and other azoles

Thiazoles and isothiazoles are privileged motifs in drug and agrochemical discovery1,2. The synthesis of these derivatives is generally approached, designed and developed on a case-by-case basis. Sometimes, the lack of robust synthesis methods to a given target can pose considerable difficulties or even thwart the preparation of specific derivatives for further study3,4. Here we report a conceptually different approach in which photochemical irradiation can be used to alter the structure of thiazoles and isothiazoles in a selective and predictable manner. On photoexcitation, these derivatives populate their π,π* singlet excited states that undergo a series of structural rearrangements, leading to an overall permutation of the cyclic system and its substituents. This means that once the initial heteroaromatic scaffold has been prepared, it can then function as an entry point to access other molecules by selective structural permutation. This approach operates under mild photochemical conditions that tolerate many chemically distinct functionalities. Preliminary findings also show the potential for extending this method to other azole systems, including benzo[d]isothiazole, indazole, pyrazole and isoxazole. This strategy establishes photochemical permutation as a powerful and convenient method for the preparation of complex and difficult-to-access derivatives from more available structural isomers.

3,3-Difluorooxetane-A Versatile Functional Group for Bioisosteric Replacements in Drug Discovery

Functional group (FG) is one of the cornerstone concepts in organic chemistry and related areas. The wide spread of bioisosterism ideas in medicinal chemistry and beyond caused a striking rise in demand for novel FGs with a defined impact on the developed compound properties. In this work, the evaluation of the 3,3-difluorooxetane unit (3,3-diFox) as a functional group for bioisosteric replacements is disclosed. A comprehensive experimental study (including multigram building block synthesis, quantification of steric and electronic properties, measurements of pKa, LogP, chemical stability, and biological evaluation of the 3,3-diFox-derived bioisostere of a drug candidate) revealed a prominent behavior of the 3,3-diFox fragment as a versatile substituent for early drug discovery programs.

Isosteric 3D Bicyclo[1.1.1]Pentane (BCP) Core-Based Lipids for mRNA Delivery and CRISPR/Cas Gene Editing

Lipid nanoparticles (LNPs) are an essential component of messenger RNA (mRNA) vaccines and genome editing therapeutics. Ionizable amino lipids, which play the most crucial role in enabling mRNA to overcome delivery barriers, have, to date, been restricted to two-dimensional (2D) architectures. Inspired by improved physicochemical properties resulting from the incorporation of three-dimensionality (3D) into small-molecule drugs, we report the creation of 3D ionizable lipid designs through the introduction of bicyclo[1.1.1]pentane (BCP) core motifs. BCP-based lipids enabled efficient in vivo mRNA delivery to the liver and spleen with significantly greater performance over 2D benzene- and cyclohexane-based analogues. Notably, lead BCP-NC2-C12 LNPs mediated ∼90% reduction in the PCSK9 serum protein level via CRISPR/Cas9 gene knockout, outperforming 2D controls and clinically used DLin-MC3-DMA LNPs at the same dose. Here, we introduce BCP-based designs with superior in vivo activity, thereby expanding the chemical scope of ionizable amino lipids from 2D to 3D and offering a promising avenue to improve mRNA and gene editing efficiency for the continued development of genetic medicines.

Ringing medicinal chemistry: The importance of 3-membered rings in drug discovery

Scaffold-based drug design has become increasingly prominent in the pharmaceutical field due to the systematic and effective approach through which it facilitates the development of novel drugs. The identification of key scaffolds provides medicinal chemists with a fundamental framework for subsequent research. With mounting evidence suggesting that increased aromaticity could impede the chances of developmental success for oral drug candidates, there is an imperative need for a more thorough exploration of alternative ring systems to mitigate attrition risks. The unique characteristics exhibited by three-membered rings have led to their application in medicinal chemistry. This review explores the use of cyclopropane-, aziridine-, thiirane-, and epoxide-containing compounds in drug discovery, focusing on their roles in approved medicines and drug candidates. Specifically, the importance of the three-membered ring systems in rending biological activity for each drug molecule was highlighted. The undeniable therapeutic value and intriguing features presented by these compounds suggest significant pharmacological potential, providing justification for their incorporation into the design of novel drug candidates.

Accurate Structure and Spectroscopic Properties of Azulene and Its Derivatives by Means of Pisa Composite Schemes and Vibrational Perturbation Theory to Second Order

The structural and spectroscopic properties in the gas phase of azulene and some of its N-bearing derivatives have been analyzed by a general computational strategy based on the recent Pisa composite schemes (PCSs). First of all, an accurate semiexperimental equilibrium structure has been derived for azulene and employed to validate the geometrical parameters delivered by different quantum chemical methods. Next, different isomerization energies (azulene to naphthalene, 1-aza-azulene to quinoline and to other isomers) have been computed by an explicitly correlated PCS version employing frozen natural orbitals. Accurate geometries have been obtained by a cheaper PCS variant based on a double-hybrid functional improved by one-parameter bond corrections, with the same functional providing also remarkable harmonic frequencies. The corresponding equilibrium rotational constants show average deviations within 0.1% from experimental results when taking into account anharmonic vibrational corrections obtained by a global hybrid functional. Therefore, reliable computational estimates have been produced for the rotational constants of several nitrogen derivatives (isomeric aza-azulenes and guaiazulene), whose non-negligible dipole moments could allow experimental microwave characterizations. An analogous approach delivers infrared spectra in remarkable agreement with their experimental counterparts for naphthalene, quinoline, and azulene, together with reliable predictions for the still-unknown spectrum of 1-aza-azulene. In addition to their intrinsic interest, the results of this paper further confirm that a very accurate yet robust and user-friendly tool is now available for aiding high-resolution spectroscopic studies of quite large systems of current technological and/or biological interest.

Synthesis, Characterization and Antimicrobial Activity of Trimethylantimony(V) Biscyanoximates, a New Family of Antimicrobials

Antimicrobial compounds play a critical role in combating microbial infections. However, the emergence of antibiotic and antifungal resistance and the scarcity of new antibiotic developments pose a significant threat and demand the discovery of new antimicrobials for both bacterial and fungal pathogens. Our previous work described the first generation (G1) of organoantimony-based compounds that showed antimicrobial activity against several bacterial and fungal pathogens. Here, we present our efforts in modifying these compounds by replacing the tetraphenyl backbone in G1 compounds with a trimethyl group, thereby generating a new series of compounds we refer to as "generation 2", G2. In addition to the novel backbone structure, we introduced three new anionic chloro-cyanoxime ligand groups, namely 2,4-diCl-PhCO-, 2,6-diCl-PhCO- and 2Cl-PhCO-, which were found to be biologically active in the past. Nine new compounds of SbMe3L2 composition were obtained in high yields and characterized by NMR, IR spectroscopies, thermogravimetric TG/DSC and X-ray single crystal analyses. The antibacterial activity of the cyanoximates was tested against three bacterial (Pseudomonas aeruginosa PAO1, Escherichia coli S17 and methicillin-resistant Staphylococcus aureus (MRSA) NRS70) and two fungal (Candida albicans strain SC5314 and Cryptococcus neoformans strain H99) pathogens. Two compounds, SbMe3(MCO)2 and SbMe3(2,4-diClPhCO)2, were active against bacterial strains and inhibited the growth of PAO1 and MRSA with MICs of 50 and 100 µg/mL, respectively. Three compounds, SbMe3(MCO)2, SbMe3(ECO)2 and SbMe3(TCO)2, were active against fungal strains and inhibited either one of or both C. albicans and C. neoformans at MICs of 2.6-66.67 μg/mL. In addition, SbMe3(TCO)2 and SbMe3(MCO)2 were fungicidal at MFC 33.33-66.67 μg/mL. Ultra-thin-layer TEM imaging suggested that SbMe3(MCO)2 targets the integrity of bacterial membranes. Overall, four of the studied G2 series compounds possess antimicrobial activity against a broad range of microbial pathogens, with particular potential against fungal pathogens, which will be explored in further studies.

Deep Lead Optimization: Leveraging Generative AI for Structural Modification

The integration of deep learning-based molecular generation models into drug discovery has garnered significant attention for its potential to expedite the development process. Central to this is lead optimization, a critical phase where existing molecules are refined into viable drug candidates. As various methods for deep lead optimization continue to emerge, it is essential to classify these approaches more clearly. We categorize lead optimization methods into two main types: goal-directed and structure-directed. Our focus is on structure-directed optimization, which, while highly relevant to practical applications, is less explored compared to goal-directed methods. Through a systematic review of conventional computational approaches, we identify four tasks specific to structure-directed optimization: fragment replacement, linker design, scaffold hopping, and side-chain decoration. We discuss the motivations, training data construction, and current developments for each of these tasks. Additionally, we use classical optimization taxonomy to classify both goal-directed and structure-directed methods, highlighting their challenges and future development prospects. Finally, we propose a reference protocol for experimental chemists to effectively utilize Generative AI (GenAI)-based tools in structural modification tasks, bridging the gap between methodological advancements and practical applications.

Revisiting Pyrimidine-Embedded Molecular Frameworks to Probe the Unexplored Chemical Space for Protein-Protein Interactions

ConspectusProtein-protein interactions (PPIs) are essential in numerous biological processes and diseases, making them attractive yet challenging drug targets. While many advances have been made in traditional drug discovery, targeting PPIs has been difficult due to a lack of specialized chemical libraries designed to modulate these interactions. Current libraries mainly focus on conventional target proteins like enzymes or receptors as substrate analogs rather than small-molecule modulators targeting PPIs. These traditional drug targets behave differently from PPIs. Conventional druggable targets have relatively small surfaces and binding pockets that have allowed them to be targeted with current libraries, but PPIs behave differently than these traditional drug targets. As a result, there is an urgent need for an innovative approach to expand the druggable space.To address this, we developed a privileged substructure-based diversity-oriented synthesis (pDOS) strategy, aimed at creating maximal skeletal diversity to explore broader biochemical space. Pyrimidine serves as the privileged substructure in our approach, which employs several strategies: (i) silver-catalyzed or iodine-mediated tandem cyclizations to generate pyrimidine-embedded polyheterocycles; (ii) diverse pairing strategies to produce pyrimidodiazepine-containing polyheterocyclic skeletons with enhanced scaffold saturation; (iii) skeletal transformation to develop pyrimidine-fused medium-sized azacycles via chemoselective cleavages or migrations of N-N or C-N bond; (iv) design of small-molecule peptidomimetics that systematically mimic three pivotal protein secondary structures using pyrimidodiazepine-based scaffolds; and (v) identification of pyrimidodiazepine-based small-molecules that allosterically inhibits the interaction between human ACE2 and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to block viral entry into host cells.Through these approaches, we generated 39 distinct pyrimidine-embedded frameworks, demonstrating significant molecular diversity validated by chemoinformatic analyses such as Tanimoto similarity and principal moment of inertia (PMI) analysis. This molecular diversity extends pyrimidine structures beyond traditional linear or bicyclic forms, creating polyheterocycles with enhanced 3D structural diversity. These novel frameworks overcome the limitation of simpler privileged scaffolds, offering promising tools for modulating PPIs.Our pDOS approach highlights how privileged structure-embedded polyheterocycles, particularly those based on pyrimidine, can effectively target previously undruggable PPIs. This strategy provides a new direction for drug discovery, allowing for the development of small molecules that operate beyond traditional drug-like rules. In addition to expanding the chemical space for PPI modulation, our pDOS strategy enables the creation of scaffolds that are particularly suited for targeting complex and dynamic protein interfaces. This innovation could significantly impact therapeutic development, offering solutions for previously intractable drug targets. By expanding the scope of pyrimidine-based scaffolds, we have opened up new possibilities for targeting PPIs and advancing chemical biology.This perspective demonstrates the potential outlines of our pDOS strategy in creating structurally diverse frameworks, offering a platform for the discovery of PPI modulators and facilitating the exploration of untapped biochemical spaces in drug development, potentially transforming the way we approach these complex biological interactions.

Iron-Mediated Dialkylation of Alkenylarenes with Benzyl Bromides

We disclose a method for the dibenzylation of alkenylarenes with benzyl bromides using iron powder. This reaction generates branched alkyl scaffolds adorned with functionalized aryl rings through the formation of two new C(sp3)-C(sp3) bonds at the vicinal carbons of alkenes. This protocol tolerates electron-rich, electron-neutral, and electron-poor benzyl bromides and alkenylarenes. Mechanistic studies suggest the formation of benzylic radical intermediates as a result of single-electron transfer from the iron, which is intercepted by alkenylarenes.

Synthesis and Fungicidal Activity Evaluation of Novel Triazole Thione/Thioether Derivatives Containing a Pyridylpyrazole Moiety

Compounds containing N-pyridylpyrazole motif have aroused interest and brought about research hotspots due to their highly-efficient insecticidal activity. The fungicidal potential of N-pyridylpyrazole derivatives has gradually been disclosed in recent years. To discover new agrochemicals with poly-heterocyclic features, a series of novel triazole thione/thioether derivatives containing pyridylpyrazole motif (8-11) was synthesized. The new compounds were identified by melting point, 1H-NMR, 13C NMR, 19F NMR, HRMS, and elemental analysis. The bioassays showed that most of the pyridylpyrazole-containing triazole thione Mannich bases possessed favorable in vitro fungicidal activity toward pathogenic fungi, such as Magnaporthe oryzae, Sclerotinia sclerotiorum, Botrytis cinerea and Fusarium verticillioides, and were comparable with those of the contrast compounds A and triadimefon. Some of them exhibited moderate to good in vivo fungicidal activity against S. sclerotiorum at 0.2 mg/mL (e. g. 8f control efficacy: 60.9±3.2 %). The SEM observation displayed that 8f might cause disruption of cell membrane and wall of S. sclerotiorum. Compounds 8a, 8c, 8f-8h, 8p and 9b can serve as promising new fungicidal agents to make further structural optimization. The findings in this article provide useful clue and guidance for the design and development of new poly-heterocyclic agrochemicals.

Dearomative hydroamination of heteroarenes catalyzed by the phenolate photocatalyst

Dearomative functionalization of heteroarenes offers an attractive and sustainable approach for the rapid construction of complex 3D heterocyclic scaffolds from planar structures. Despite progress in this field, dearomative amination of heteroarenes via a radical anion intermediate remains a challenge. Here, we report a photoredox-catalyzed dearomative hydroamination of heteroarenes with hydrazodiformates under mild and transition-metal-free reaction conditions. Various benzofurans and benzothiophenes can efficiently participate in this transformation. A series of mechanistic experiments revealed that heteroaryl radical anions are the crucial intermediates, generated through photo-induced electron transfer between the excited phenolate photocatalyst and heteroarenes.

Motivations for enrollment in a COVID-19 ring-based post-exposure prophylaxis trial: qualitative examination of participant experiences

BACKGROUND

Ring-based studies are a novel research design commonly used for research involving infectious diseases: contacts of newly infected individuals form a ring that is targeted for interventions (e.g., vaccine, post-exposure prophylaxis). Given the novelty of the research design, it is critical to obtain feedback from participants on their experiences with ring-based studies to help with the development of future trials.

METHODS

In 2021, we conducted 26 semi-structured interviews with adult participants of a COVID-19 ring-based post-exposure prophylaxis trial based in Canada. We applied a purposive sampling approach and electronically recruited participants who tested positive for COVID-19 (Index Cases) and either agreed or declined for the study team to contact their potentially exposed contacts. We also included individuals who participated in the trial after being potentially exposed to an Index Case (known as Ring Members), and those who declined to participate after potential exposure. The methodological design of semi-structured interviews allowed participants to share their opinions and experiences in the trial (e.g., elements they enjoyed and disliked regarding their participation in the study).

RESULTS

The majority of participants in our study were women (62%) and the average age was 37.3 years (SD = 13.2). Overall, participants reported being highly satisfied with partaking in the ring-based trial. Notably, no substantial complaints were voiced about the trial's design involving contact after exposure. The most common reason of satisfaction was the knowledge of potentially helping others by advancing knowledge for a greater cause (e.g., development of potential treatment to prevent SARS-CoV-2 infection). Other reasons were curiosity about participating in a trial, and an activity to fill free time during the pandemic. A central element of dislike was confusion about instructions with the trial (e.g., independent at home SARS-CoV-2 testing). Additionally, maintaining confidentiality was a crucial concern for participants, who sought assurance that their data would not be shared beyond the scope of the study.

CONCLUSIONS

Our results have the potential to inform future research, including clinical trials such as ring-based studies, by incorporating insights from participants' experiences into the development of study protocols. Despite some protocol-related challenges, participants expressed high satisfaction, driven by the desire to advance science and potentially aid others.

Synthesis of 1-Substituted Bicyclo[2.1.1]hexan-2-ones via a Sequential SmI2-Mediated Pinacol Coupling and Acid-Catalyzed Pinacol Rearrangement Reaction

A two-step procedure, combining a SmI2-mediated transannular pinacol coupling reaction with an acid-catalyzed pinacol rearrangement process, was employed to prepare a diverse range of 1-substituted bicyclo[2.1.1]hexan-5-ones from cyclobutanedione derivatives. To underscore the significance of these bicyclic ketones in drug synthesis, an sp3-rich analog of nitazoxanide, a well-known antiparasitic and antiviral agent, was synthesized.

Synthesis of 3,3-Disubstituted Thietane Dioxides

4-Membered heterocycles have been increasingly exploited in medicinal chemistry and, as small polar motifs, often show important influence on activity and physicochemical properties. Thietane dioxides similarly offer potential in both agricultural and pharmaceutical applications but are notably understudied. Here we report a divergent approach to 3,3-disubstituted thietane dioxide derivatives by forming carbocations on the 4-membered ring with catalytic Lewis or Brønsted acids. Benzylic tertiary alcohols of the thietane dioxides are coupled directly with arenes, thiols, and alcohols.

Diffusing on Two Levels and Optimizing for Multiple Properties: A Novel Approach to Generating Molecules With Desirable Properties

In the past decade, Artificial Intelligence (AI) driven drug design and discovery has been a hot research topic in the AI area, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest diffusion-based models. However, most existing models pursue mainly the basic properties like validity and uniqueness of the generated molecules, a few go further to explicitly optimize one single important molecular property (e.g. QED or PlogP), which makes most generated molecules little usefulness in practice. In this paper, we present a novel approach to generating molecules with desirable properties, which expands the diffusion model framework with multiple innovative designs. The novelty is two-fold. On the one hand, considering that the structures of molecules are complex and diverse, and molecular properties are usually determined by some substructures (e.g. pharmacophores), we propose to perform diffusion on two structural levels: molecules and molecular fragments respectively, with which a mixed Gaussian distribution is obtained for the reverse diffusion process. To get desirable molecular fragments, we develop a novel electronic effect based fragmentation method. On the other hand, we introduce two ways to explicitly optimize multiple molecular properties under the diffusion model framework. First, as potential drug molecules must be chemically valid, we optimize molecular validity by an energy-guidance function. Second, since potential drug molecules should be desirable in various properties, we employ a multi-objective mechanism to optimize multiple molecular properties simultaneously. Extensive experiments with two benchmark datasets QM9 and ZINC250 k show that the molecules generated by our proposed method have better validity, uniqueness, novelty, Fréchet ChemNet Distance (FCD), QED, and PlogP than those generated by current SOTA models.

High-throughput screening of more than 30,000 compounds for anthelmintics against gastrointestinal nematode parasites

Gastrointestinal nematodes (GINs) are amongst the most common parasites of humans, livestock, and companion animals. GIN parasites infect 1-2 billion people worldwide, significantly impacting hundreds of millions of children, pregnant women, and adult workers, thereby perpetuating poverty. Two benzimidazoles with suboptimal efficacy are currently used to treat GINs in humans as part of mass drug administrations, with many instances of lower-than-expected or poor efficacy and possible resistance. Thus, new anthelmintics are urgently needed. However, screening methods for new anthelmintics using human GINs typically have low throughput. Here, using our novel screening pipeline that starts with human hookworms, we screened 30,238 unique small molecules from a wide range of compound libraries, including ones with generic diversity, repurposed drugs, natural derivatives, known mechanisms of action, as well as multiple target-focused libraries (e.g., targeting kinases, GPCRs, and neuronal proteins). We identified 55 compounds with broad-spectrum activity against adult stages of two evolutionary divergent GINs, hookworms ( Ancylostoma ceylanicum ) and whipworms ( Trichuris muris ). Based on known databases, the targets of these 55 compounds were predicted in nematode parasites. One novel scaffold from the diversity set library, F0317-0202, showed good activity (high motility inhibition) against both GINs. To better understand this novel scaffold's structure-activity relationships (SAR), we screened 28 analogs and created SAR models highlighting chemical and functional groups required for broad-spectrum activity. These studies validate our new and efficient screening pipeline at the level of tens of thousands of compounds and provide an important set of new GIN-active compounds for developing novel and broadly-active anthelmintics.

Direct C-H functionalisation of azoles via Minisci reactions

Azoles have widespread applications in medicinal chemistry; for example, thiazoles, imidazoles, benzimidazoles, isoxazoles, tetrazoles and triazoles appear in the top 25 most frequently used N-heterocycles in FDA-approved drugs. Efficient routes for the late-stage C-H functionalisation of azole cores would therefore be highly desirable. The Minisci reaction, a nucleophilic radical addition reaction onto N-heterocyclic bases, is a direct C-H functionalisation reaction that has the potential to be a powerful method for C-H functionalisations of azole scaffolds. However, azoles have not been as widely studied as substrates for modern Minisci-type reactions as they are often more electron-rich and thus more challenging substrates compared to electron-poor 6-membered N-heterocycles such as quinolines, pyrazines and pyridines typically used in Minisci reactions. Nevertheless, with the prevalence of azole scaffolds in drug design, the Minisci reaction has the potential to be a transformative tool for late-stage C-H functionalisations to efficiently access decorated azole motifs. This review thus aims to give an overview of the C-H functionalisation of azoles via Minisci-type reactions, highlighting recent progress, existing limitations and potential areas for growth.

Innovative Strategies and Methodologies in Antimicrobial Peptide Design

Multiple lines of research have led to the hypothesis that antimicrobial peptides (AMPs) are an important component of the innate immune response, playing a vital role in the defense against a wide range of infectious diseases. In this review, we explore the occurrence and availability of antimicrobial proteins and peptides across various species, highlighting their natural abundance and evolutionary significance. The design of AMPs has been driven by the identification of key structural and functional features, which are essential for optimizing their antimicrobial activity and reducing toxicity to host cells. We discuss various approaches, including rational design, high-throughput screening, and computational modeling, that have been employed to develop novel AMPs with enhanced efficacy. A particular focus is given to the identification and characterization of peptide fragments derived from naturally occurring host defense proteins, which offer a promising avenue for the discovery of new AMPs. The incorporation of artificial intelligence (AI) and machine learning (ML) tools into AMP research has further accelerated the identification, optimization, and application of these peptides. This review also discusses the current status and therapeutic potential of AMPs, emphasizing their role in addressing the growing issue of antibiotic resistance. The conclusion highlights the importance of continued research and innovation in AMP development to fully harness their potential as next-generation antimicrobial agents.

Synthesis and evaluation of chemical linchpins for highly selective CK2α targeting

Casein kinase-2 (CK2) are serine/threonine kinases with dual co-factor (ATP and GTP) specificity, that are involved in the regulation of a wide variety of cellular functions. Small molecules targeting CK2 have been described in the literature targeting different binding pockets of the kinase with a focus on type I inhibitors such as the recently published chemical probe SGC-CK2-1. In this study, we investigated whether known allosteric inhibitors binding to a pocket adjacent to helix αD could be combined with ATP mimetic moieties defining a novel class of ATP competitive compounds with a unique binding mode. Linking both binding sites requires a chemical linking moiety that would introduce a 90-degree angle between the ATP mimetic ring system and the αD targeting moiety, which was realized using a sulfonamide. The synthesized inhibitors were highly selective for CK2 with binding constants in the nM range and low micromolar activity. While these inhibitors need to be further improved, the present work provides a structure-based design strategy for highly selective CK2 inhibitors.

Asymmetric Transfer Hydrogenation of gem-Difluorocyclopropenyl Ketones: The Synthesis and Functionalization of Enantioenriched cis gem-Difluorocyclopropyl Ketones

The asymmetric transfer hydrogenation of gem-difluorocyclopropenyl ketones, catalyzed by a Noyori-Ikariya ruthenium complex, was developed to access substituted optically enriched cis-disubstituted gem-difluorocyclopropyl ketones, and the value of these latter building blocks was illustrated by the synthesis of heterocycles fused to the difluorocyclopropyl moiety.

Activity of Organoboron Compounds against Biofilm-Forming Pathogens

Bacteria have evolved and continue to change in response to environmental stressors including antibiotics. Antibiotic resistance and the ability to form biofilms are inextricably linked, requiring the continuous search for alternative compounds to antibiotics that affect biofilm formation. One of the latest drug classes is boron-containing compounds. Over the last several decades, boron has emerged as a prominent element in the field of medicinal chemistry, which has led to an increasing number of boron-containing compounds being considered as potential drugs. The focus of this review is on the developments in boron-containing organic compounds (BOCs) as antimicrobial/anti-biofilm probes and agents.

Chemoinformatic Characterization of NAPROC-13: A Database for Natural Product 13C NMR Dereplication

Natural products (NPs) are secondary metabolites of natural origin with broad applications across various human activities, particularly the discovery of bioactive compounds. Structural elucidation of new NPs entails significant cost and effort. On the other hand, the dereplication of known compounds is crucial for the early exclusion of irrelevant compounds in contemporary pharmaceutical research. NAPROC-13 stands out as a publicly accessible database, providing structural and 13C NMR spectroscopic information for over 25 000 compounds, rendering it a pivotal resource in natural product (NP) research, favoring open science. This study seeks to quantitatively analyze the chemical content, structural diversity, and chemical space coverage of NPs within NAPROC-13, compared to FDA-approved drugs and a very diverse subset of NPs, UNPD-A. Findings indicated that NPs in NAPROC-13 exhibit properties comparable to those in UNPD-A, albeit showcasing a notably diverse array of structural content, scaffolds, ring systems of pharmaceutical interest, and molecular fragments. NAPROC-13 covers a specific region of the chemical multiverse (a generalization of the chemical space from different chemical representations) regarding physicochemical properties and a region as broad as UNPD-A in terms of the structural features represented by fingerprints.

GPCRSPACE: A New GPCR Real Expanded Library Based on Large Language Models Architecture and Positive Sample Machine Learning Strategies

The quest for novel therapeutics targeting G protein-coupled receptors (GPCRs), essential in numerous physiological processes, is crucial in drug discovery. Despite the abundance of GPCR-targeting drugs, many receptors lack selective modulators, indicating a significant untapped therapeutic potential. To bridge this gap, we introduce GPCRSPACE, a novel GPCR-focused purchasable real chemical library developed using the G protein-coupled receptors large language models (GPCR LLM) architecture. Different from traditional machine learning models, GPCR LLM uses a positive sample machine learning strategy for training and does not need to construct any negative samples. This not only reduces false negatives but also reduces the time to label negative samples. GPCR LLM accelerates the identification and screening of potential GPCR-interactive compounds by learning the chemical space of GPCR-targeting molecules. GPCRSPACE, built on GPCR LLM, outperforms existing chemical data sets in synthesizability, structural diversity, and GPCR-likeness, making it a valuable tool for GPCR drug discovery.

Anti-Schistosomal activity and ADMET properties of 1,2,5-oxadiazinane-containing compound synthesized by visible-light photoredox catalysis

The incorporation of saturated nitrogen-containing heterocycle 1,2,5-oxadiazinane into small molecules represents a compelling avenue in drug discovery due to its unexplored behavior within biological systems and incomplete protocols for synthesis. In this study, we present 1,2,5-oxadiazinane, an innovative heterocyclic bioisostere of piperizin-2-one and novel chemotype of the anti-schistosomal drug praziquantel (PZQ), which has been the only clinical drug available for three decades. PZQ is associated with significant drawbacks, including poor solubility, a bitter taste, and low metabolic stability. Therefore, the discovery of a new class of anti-schistosomal agents is imperative. To address this challenge, we introduce a pioneering method for the synthesis of 1,2,5-oxadiazinane derivatives through the cycloaddition of nitrones with N,N,N',N'-tetraalkyldiaminomethane in the presence of an IrIII complex photosensitizer. This transformative reaction offers a streamlined route to various kinds of 1,2,5-oxadiazinanes that is characterized by mild reaction conditions and broad substrate scope. Mechanistic investigations suggest that the photoredox pathway underlies the [3 + 3] photocycloaddition process. Thus, based on bioisosteric replacement, we identified a remarkable molecule as a new chemotype of a potent anti-schistosomal compound that not only exhibits superior solubility, but also retains the potent biological activity inherent to PZQ.

Direct C-H amidation of 1,3-azoles: light-mediated, photosensitiser-free vs. thermal

We have developed one thermal and one light-mediated method for direct Minisci-type C-H amidation of 1,3-azoles, which are applicable to thiazoles, benzothiazoles, benzimidazoles, and for the first time, imidazoles. The new visible light-mediated approach can be rendered photosensitiser/photocatalyst-free and likely proceeds via an electron donor-acceptor (EDA) complex, the first direct Minisci-type amidation to do so.

Regio- and Diastereoselective Synthesis of Polysubstituted Piperidines Enabled by Boronyl Radical-Catalyzed (4+2) Cycloaddition

Piperidines are widely present in small molecule drugs and natural products. Despite many methods have been developed for their synthesis, new approaches to polysubstituted piperidines are highly desirable. This work presents a radical (4+2) cycloaddition reaction for synthesis of piperidines featuring dense substituents at 3,4,5-positions that are not readily accessible by known methods. Using commercially available diboron(4) compounds and 4-phenylpyridine as the catalyst precursors, the boronyl radical-catalyzed cycloaddition between 3-aroyl azetidines and various alkenes, including previously unreactive 1,2-di-, tri-, and tetrasubstituted alkenes, has delivered the polysubstituted piperidines in generally high yield and diastereoselectivity. The reaction also features high modularity, atom economy, broad substrate scope, metal-free conditions, simple catalysts and operation. The utilization of the products has been demonstrated by selective transformations. A plausible mechanism, with the ring-opening of azetidine as the rate-limiting step, has been proposed based on the experimental and computational results.

Enantioselective formal (3 + 3) cycloaddition of bicyclobutanes with nitrones enabled by asymmetric Lewis acid catalysis

The absence of catalytic asymmetric methods for synthesizing chiral (hetero)bicyclo[n.1.1]alkanes has hindered their application in new drug discovery. Here we demonstrate the achievability of an asymmetric polar cycloaddition of bicyclo[1.1.0]butane using a chiral Lewis acid catalyst and a bidentate chelating bicyclo[1.1.0]butane substrate, as exemplified by the current enantioselective formal (3 + 3) cycloaddition of bicyclo[1.1.0]butanes with nitrones. In addition to the diverse bicyclo[1.1.0]butanes incorporating an acyl imidazole group or an acyl pyrazole moiety, a wide array of nitrones are compatible with this Lewis acid catalysis, successfully assembling two congested quaternary carbon centers and a chiral aza-trisubstituted carbon center in the pharmaceutically important hetero-bicyclo[3.1.1]heptane product with up to 99% yield and >99% ee.

Isothiourea-Catalysed Acylative Dynamic Kinetic Resolution of Tetra-substituted Morpholinone and Benzoxazinone Lactols

The development of methods to allow the selective acylative dynamic kinetic resolution (DKR) of tetra-substituted lactols is a recognised synthetic challenge. In this manuscript, a highly enantioselective isothiourea-catalysed acylative DKR of tetra-substituted morpholinone and benzoxazinone-derived lactols is reported. The scope and limitations of this methodology have been developed, with high enantioselectivity and good to excellent yields (up to 89 %, 99 : 1 er) observed across a broad range of substrate derivatives incorporating substitution at N(4) and C(2), di- and spirocyclic substitution at C(5) and C(6), as well as benzannulation (>35 examples in total). The DKR process is amenable to scale-up on a 1 g laboratory scale. The factors leading to high selectivity in this DKR process have been probed through computation, with an N-C=O⋅⋅⋅isothiouronium interaction identified as key to producing ester products in highly enantioenriched form.

Light-enabled scalable synthesis of bicyclo[1.1.1]pentane halides and their functionalizations

In 2012, bicyclo[1.1.1]pentanes were demonstrated to be bioisosteres of the benzene ring. Here, we report a general scalable reaction between alkyl iodides and propellane that provides bicyclo[1.1.1]pentane iodides in milligram, gram and even kilogram quantities. The reaction is performed in flow and requires just light; no catalysts, initiators or additives are needed. The reaction is clean enough that, in many cases, evaporation of the reaction mixture provides products in around 90% purity that can be directly used in further transformations without any purification. Combined with the subsequent functionalization, >300 bicyclo[1.1.1]pentanes for medicinal chemistry have been prepared. So far, this is the most general and scalable approach towards functionalized bicyclo[1.1.1]pentanes.

Cyclopropanation with Non-Stabilized Carbenes via Ketyl Radicals

A radical mechanism enables simple and robust access to nonstabilized, alkyl iron carbenes for novel (2 + 1) cycloadditions. This Fe-catalyzed strategy employs simple, aliphatic aldehydes as carbene precursors in a practical, efficient, and stereoselective cyclopropanation. This air- and water-tolerant method permits convenient generation of iron carbenes and coupling to an exceptionally wide range of sterically and electronically diverse alkenes (nucleophilic, electrophilic, and neutral). A transient ketyl radical intermediate is key to accessing and harnessing this rare, alkyl iron carbene reactivity. Mechanistic experiments confirm the (a) intermediacy of ketyl radicals, (b) iron carbene formation by radical capture, and (c) nonconcerted nature of the (2 + 1) cycloaddition.

A guide to bullvalene stereodynamics

Here, we analyze the stereodynamic properties of bullvalenes using principal moments of inertia and exit vector plots to draw comparisons with commonly used ring systems in medicinal chemistry. To aid analyses, we first classify (i) the four elementary rearrangement steps available to substituted bullvalenes, which (ii) can be described by applying positional descriptors (α, β, γ, and δ) to the substituents. We also (iii) derive an intuitive equation to calculate the number of isomers for a given bullvalene system. Using DFT-modelled structures for di-, tri-, and tetrasubstituted bullvalenes, generated using a newly developed computational tool (bullviso), we show that their 3D shapes and the exit vectors available from the bullvalene scaffold make them comparable to other bioisosteres currently used to replace planar aromatic ring systems in drug discovery. Unlike conventional ring systems, the shapeshifting valence isomerism of bullvalenes gives rise to numerous shapes and substituent relationships attainable as a concentration-independent dynamic covalent library from a single compound. We visualize this property by applying population weightings to the principal moments of inertia and exit vector analyses to reflect the relative thermodynamic stabilities of the available isomers.