Rings in Clinical Trials and Drugs: Present and Future

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.

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.

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.

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.

"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.

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.

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.

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.

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.

Fe-Catalyzed Fluoroalkyl(hetero)arylation of Vinyl Azaarenes: Rapid and Modular Synthesis of Unsymmetrical 1,1-Bis(hetero)arylalkanes

In contrast to transition-metal-catalyzed difunctionalization of activated alkenes, selective alkylarylation of vinyl azaarenes is underdeveloped. Consequently, the lack of modular and rapid syntheses of 1,1-bis(hetero)arylalkanes limits their exploration in medicinal chemistry. Herein we report a protocol using commercially available iron salts, bisphosphine ligands, fluoroalkyl halides, and Grignard reagents that enables the selective 1,2-fluoroalkyl(hetero)arylation of vinyl azaarenes. We demonstrate the versatility and robustness of the method through the selective synthesis of a range of unsymmetrical 1,1-bis(hetero)arylalkenes, including pyridine N-oxides, triazoles, pyrazines, carbazoles, indazoles, and 1,2-azaborines. Mechanistic insights from experimental and computational investigations support a radical pathway and provide insights into the role of non-covalent interactions in iron catalysis.

Combining (CH2O)n and (NH4)2CO3 as a Formamidine Equivalent for "Four-in-One" Synthesis of Fluoroalkylated 2-H-Pyrimidines

Multicomponent reactions hold the potential to maximize the synthetic efficiency in the preparation of diverse and complex molecular scaffolds. An unprecedented formal [3+1+1+1] annulation approach for the one-step synthesis of fluoroalkylated 2-H-pyrimidines commencing from perfluoroalkyl alkenes, paraformaldehyde, and ammonium carbonate is described. By harnessing readily accessible (CH2O)n and cheap (NH4)2CO3 as a formamidine surrogate, this method effectively replaces traditionally preformed amidines with a pyrimidine assembly. The multicomponent reaction proceeds in a step-economical, operationally simple, metal-free, and additive-free manner, featuring a broad substrate scope, excellent functional group compatibility, and scalability. The potential for the synthetic elaboration of the obtained 2-H-pyrimidine is further demonstrated in the alkylation and vinylation of its C2 position.

Shining light on the nitro group: distinct reactivity and selectivity

The nitro moiety is an indispensable functional group in organic synthesis due to its facile introduction and reduction to the corresponding amines for a plethora of organic transformations. Owing to its distinct electronegative and conventional properties, it has been used for activated aromatic nucleophilic substitution (SNAr) reactions, Smiles reactions, Henry reactions, acyl anion equivalents, etc. Recently, the excellent photochemical properties of nitroarenes have been rediscovered by several groups, and their untapped potential in organic synthesis under UV or visible light irradiation has been exploited. Photoexcited nitroarenes can undergo facile reduction to amines, azo-coupling, metal-free reductive C-N coupling with boronic acids via a 1,2-boronate shift, hydrogen atom transfer (HAT), oxygen atom transfer for anaerobic oxidation of organic molecules, molecular editing via nitrene intermediates, denitrative coupling of β-nitrostyrene, radical α-alkylation of nitroalkanes, etc. They have also been used as a photolabile protecting group in medicinal chemistry and chemical biology applications. Here, we summarise the recent findings on visible-light-mediated transformations involving nitro-containing organic molecules.

A Radical Strategy for the Alkylation of Amides with Alkyl Halides by Merging Boryl Radical-Mediated Halogen-Atom Transfer and Copper Catalysis

Amide alkylation is a fundamental process in organic chemistry. However, the low nucleophilicity of amides means that divergent coupling with alkyl electrophiles is often not achievable. To circumvent this reactivity challenge, individual amine synthesis followed by amidation with standard coupling agents is generally required. Herein, we demonstrate a radical solution to this challenge by using an amine-borane complex and copper catalysis under oxidative conditions. While borohydride reagents are generally used as reducing agents in ionic chemistry, their conversion into amine-ligated boryl radicals diverts their reactivity toward halogen-atom transfer. This enables the conversion of alkyl halides into the corresponding alkyl radicals for amide functionalization via copper catalysis. The process is applicable to the N-alkylation of primary amides employing unactivated alkyl iodides and bromides, and it was also showcased in the late-state functionalization of both complex amide- and halide-containing drugs.

Palladium-Catalyzed Ligand-Controlled Switchable Hetero-(5 + 3)/Enantioselective [2σ+2σ] Cycloadditions of Bicyclobutanes with Vinyl Oxiranes

For nearly 60 years, significant research efforts have been focused on developing strategies for the cycloaddition of bicyclobutanes (BCBs). However, higher-order cycloaddition and catalytic asymmetric cycloaddition of BCBs have been long-standing formidable challenges. Here, we report Pd-catalyzed ligand-controlled, tunable cycloadditions for the divergent synthesis of bridged bicyclic frameworks. The dppb ligand facilitates the formal (5+3) cycloaddition of BCBs and vinyl oxiranes, yielding valuable eight-membered ethers with bridged bicyclic scaffolds in 100% regioselectivity. The Cy-DPEphos ligand promotes selective hetero-[2σ+2σ] cycloadditions to access pharmacologically important 2-oxabicyclo[3.1.1]heptane (O-BCHeps). Furthermore, the corresponding catalytic asymmetric synthesis of O-BCHeps with 94-99% ee has been achieved using chiral (S)-DTBM-Segphos, representing the first catalytic asymmetric cross-dimerization of two strained rings. The obtained O-BCHeps are promising bioisosteres for ortho-substituted benzenes.

Stereodivergent Synthesis of Pyridyl Cyclopropanes via Enzymatic Activation of Pyridotriazoles

Hemoproteins have recently emerged as powerful biocatalysts for new-to-nature carbene transfer reactions. Despite this progress, these strategies have remained largely limited to diazo-based carbene precursor reagents. Here, we report the development of a biocatalytic strategy for the stereoselective construction of pyridine-functionalized cyclopropanes via the hemoprotein-mediated activation of pyridotriazoles (PyTz) as stable and readily accessible carbene sources. This method enables the asymmetric cyclopropanation of a variety of olefins, including electron-rich and electrodeficient ones, with high activity, high stereoselectivity, and enantiodivergent selectivity, providing access to mono- and diarylcyclopropanes that incorporate a pyridine moiety and thus two structural motifs of high value in medicinal chemistry. Mechanistic studies reveal a multifaceted role of 7-halogen substitution in the pyridotriazole reagent toward favoring multiple catalytic steps in the transformation. This work provides the first example of asymmetric olefin cyclopropanation with pyridotriazoles, paving the way to the exploitation of these attractive and versatile reagents for enzyme-catalyzed carbene-mediated reactions.

Light-Driven Intramolecular Cyclopropanation of Alkene-Tethered N-Tosylhydrazones: Synthesis of Fused-Cyclopropane γ-Lactones

Fused-cyclopropane ring-containing γ-lactone compounds are versatile building blocks in many fields, including the synthesis of biologically active compounds. Here, we report the light-driven intramolecular cyclopropanation of alkene-tethered N-tosylhydrazones in the presence of Cs2CO3 and visible light. We have synthesized various electronically and sterically substituted and heterocyclic-containing fused-(spiro)cyclopropane γ-lactone compounds in good yields under transition metal-free conditions using a radical-free approach. In addition, the one-pot synthesis of fused-cyclopropane γ-lactones from α-ketoesters and their synthetic utility are also presented.

Rapid Access to Divergent Fused Polycycles Via One-Pot A3 Coupling and Intramolecular Diels-Alder Reaction

Divergent nitrogen-containing fused polycyclic ring systems are constructed from simple starting materials via a one-pot aldehyde-alkyne-amine (A3) coupling and intramolecular Diels-Alder reaction. This domino reaction directly furnishes linear 5/5/5 and 5/5/6, or nonlinear 5/5/6/5, polycyclic rings containing an oxa-bridged fused 5/5 bicycle and a 1,6-enyne substructure. One-step derivation of the oxa-bridged 5/5 bicycle leads to a polyfunctionalized 5/5 bicycle with tetrahydrofuran fused back-to-back to pyrroline or a 6/5 bicycle with the hexahydro-1H-isoindole structure, while cycloisomerizing the enyne substructure adds an extra fused 5-membered ring to afford functionalized linear 5/5/5/5 or 5/5/5/5/5 fused ring systems from selected substrates. In addition, the one-pot product can be designed so that the alkyne moiety is hydroalkoxylated to form an additional heterocyle in a linear 5/5/5/6 or nonlinear 5/5/6/5/5 ring system. This diversity-oriented synthetic approach thus allows rapid access to an under-explored structural space for discovery of new biological or non-biological activities or functions.

Identifying High-Quality Leads among Screened Anticancerous Compounds Using SMILES Representations

Cancer is a lethal disease that affects numerous people worldwide. Chemotherapy stands as one of the most effective treatment regimens to combat cancer. Nevertheless, anticancer drugs face a high failure rate due to safety and efficacy issues. Drug failure could be subdued by instigating drug leads with reduced toxicity and enhanced efficacy. Computer-aided drug discovery endorses drug leads in manoeuvring protein and ligand structures or representations. Simplified molecular input line entry system (SMILES) is a linear notation representing the three-dimensional structure of a molecule using symbols and alphanumeric characters. SMILES representation hoards rings and scaffold structures in its depiction. Mining ring and scaffold patterns from molecular SMILES would assist in ascertaining biological properties based on molecular patterns. Moreover, the emergence of artificial intelligence (AI) technologies would accelerate identification of efficient anticancer drug leads. AI algorithms proclaimed for their pattern recognition ability could be employed for identifying molecular patterns from SMILES representation, thereby enabling property prediction. Consequently, we developed a multilayer perceptron (MLP) model for the prediction of anticancer activity using SMILES of NCI-60 cancer growth inhibition data. Furthermore, the top 8 frequent scaffolds were identified on preliminary analysis of cancer growth inhibition data and ChEMBL drugs. The developed MLP model classified anticancer and nonanticancer compounds with a classification accuracy of 0.92. Also, benchmarking of the developed model with machine learning algorithms exhibited better performance of the MLP model.

Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery

Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.

Ligand Effects in Carboxylic Ester- and Aldehyde-Assisted β-C-H Activation in Regiodivergent and Enantioselective Cycloisomerization-Hydroalkenylation and Cycloisomerization-Hydroarylation, and [2 + 2 + 2]-Cycloadditions of 1,6-Enynes

Herein, we report room temperature, atom-economic protocols for high regio- and enantioselective tandem cycloisomerization-hydroarylation and cycloisomerization-hydroalkenylation of 1,6-enynes leading to vicinal carba-functionalized pyrrolidines, tetrahydrofurans, and cyclopentanes. The latter steps in these processes involve carbonyl-coordination-assisted ortho-C-H activation of aromatic aldehydes and esters, and, a similar, yet rarely seen, β-C-H activation in the case of the acrylates. Synthetically useful enantioselective versions of such reactions are rare and are limited to the C2-H activation of indoles and pyrroles. A similar reaction is also observed with N-vinylphthalimide, which also has a carbonyl group suitable for C-H activation. A dibenzooxaphosphole ligand, (2S,2S',3S,3S')-MeO-BIBOP was uniquely identified as crucial to achieving the challenging regio- and enantioselectivity. This methodology gives access to substituted five-membered carbo- and heterocyclic compounds in good yields and excellent enantioselectivities under a low catalyst loading. A primary KIE of 3.5 is observed in an intermolecular competition experiment with methyl benzoate and d5-methyl benzoate, which indicates that the C-H cleavage is the turnover-limiting step of this process. Unlike the acrylates, which undergoes exclusive hydroalkenylation, a β, γ-unsaturated ester, methyl but-3-enoate, undergoes the highly enantioselective cycloisomerization-coupling sequence with a 1,6-enyne giving either a [2 + 2 + 2]-cycloaddition with (S, S)-BDPP or hydroalkenylation with (2S,2'S,3S,3'S)-MeO-BIBOP depending on the ligand employed. The (E)-configuration of the newly formed double bond at the terminal alkynyl carbon (of the starting enyne) in the hydroalkenylation product of β,γ-unsaturated ester suggests a more classical migratory insertion-β-hydride elimination route for the formation of this product.

Switchable and Chemoselective Arene Hydrogenation for Efficient Late Stage Applications

The incorporation of three-dimensional structures into drug molecules has demonstrated significant improvements in clinical success. Late-stage saturation of drug molecules provides a direct pathway for this transformation. However, achieving selective and controllable reduction of aromatic rings remains challenging, particularly when multiple aromatic rings coexist. Herein, we present the switchable and chemoselective hydrogenation of benzene and pyridine rings. The utility of the protocol has been comprehensively investigated in diversified substrates with the assistance of a fragment-screening technique. This approach provides convenient access to a diverse array of cyclohexane and piperidine compounds, prevalent in various bioactive molecules and drugs. Furthermore, it discloses promising avenues for applications in the late-stage switchable saturation of drugs, facilitating an increase in the fraction of sp3-carbons which holds the potential to enhance the medicinal properties of drugs.

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Deep simulated annealing for the discovery of novel dental anesthetics with local anesthesia and anti-inflammatory properties

Multifunctional therapeutics have emerged as a solution to the constraints imposed by drugs with singular or insufficient therapeutic effects. The primary challenge is to integrate diverse pharmacophores within a single-molecule framework. To address this, we introduced DeepSA, a novel edit-based generative framework that utilizes deep simulated annealing for the modification of articaine, a well-known local anesthetic. DeepSA integrates deep neural networks into metaheuristics, effectively constraining molecular space during compound generation. This framework employs a sophisticated objective function that accounts for scaffold preservation, anti-inflammatory properties, and covalent constraints. Through a sequence of local editing to navigate the molecular space, DeepSA successfully identified AT-17, a derivative exhibiting potent analgesic properties and significant anti-inflammatory activity in various animal models. Mechanistic insights into AT-17 revealed its dual mode of action: selective inhibition of NaV1.7 and 1.8 channels, contributing to its prolonged local anesthetic effects, and suppression of inflammatory mediators via modulation of the NLRP3 inflammasome pathway. These findings not only highlight the efficacy of AT-17 as a multifunctional drug candidate but also highlight the potential of DeepSA in facilitating AI-enhanced drug discovery, particularly within stringent chemical constraints.

Unpredictable Dynamic Behaviour of Ruthenium Chelate Pyrrole Derivatives

Reaction of [Ru(H)2(CO)(PPh3)3] 1 with an equimolar amount of pyrrole-2-carboxylic acid (H2L1) leads to the homoleptic chelate derivative k2(O,O)-[RuH(CO)(HL1)(PPh3)2] 2. Prolonged acetonitrile refluxing promotes an unusual k2(O,O)- → k2(N,O)- dynamic chelate conversion, forming a neutral, stable, air- and moisture- insensitive, solvento-species k2(N,O)-[Ru(MeCN)(CO)(L1)(PPh3)2] 3. Analogously, reaction of 1 with the pyrrole-2-carboxyaldehyde (HL2) affords k2(N,O)-[RuH(CO)(HL2)(PPh3)2] 4, 5, as a couple of functional isomers. Optimized reaction conditions such as temperature and solvent polarity allow the isolation of dominant configurations. Structure 5 is a pyrrolide Ru-carbaldehyde, obtained from cyclization of the pendant CHO function, whereas species 4 can be viewed as an ethanoyl-conjugated Ru-pyrrole. Derivatives 3-5 were characterized by single crystal X-ray diffraction, ESI-Ms, IR, and NMR spectroscopy, indicating distinct features for the Ru-bonded pyrrolyl groups. DFT computational results, coplanarity, bond equalization, and electron delocalization along the fused five-membered rings support aromatic features. In accordance with the antisymbiotic trans-influence, both the isolated isomers 4 and 5 disclose CO ligands opposite to N- or O-anionic groups. The quantitative Mayer bond order evidences a stabilizing backbonding effect. Antibacterial and antifungal trials on Gram-positive (Staphylococcus aureus), Gram-negative (Escherichia coli), and Candida albicans were further carried out.

Electrochemical synthesis of peptide aldehydes via C‒N bond cleavage of cyclic amines

Peptide aldehydes are crucial biomolecules essential to various biological systems, driving a continuous demand for efficient synthesis methods. Herein, we develop a metal-free, facile, and biocompatible strategy for direct electrochemical synthesis of unnatural peptide aldehydes. This electro-oxidative approach enabled a step- and atom-economical ring-opening via C‒N bond cleavage, allowing for homoproline-specific peptide diversification and expansion of substrate scope to include amides, esters, and cyclic amines of various sizes. The remarkable efficacy of the electro-synthetic protocol set the stage for the efficient modification and assembly of linear and macrocyclic peptides using a concise synthetic sequence with racemization-free conditions. Moreover, the combination of experiments and density functional theory (DFT) calculations indicates that different N-acyl groups play a decisive role in the reaction activity.

De-epimerizing DyKAT of β-lactones generated by isothiourea-catalysed enantioselective [2 + 2] cycloaddition

An enantioselective isothiourea-catalysed [2 + 2] cycloaddition of C(1)-ammonium enolates with pyrazol-4,5-diones is used to construct spirocyclic β-lactones in good yields, excellent enantioselectivity (99 : 1 er) but with modest diastereocontrol (typically 70 : 30 dr). Upon ring-opening with morpholine or alternative nucleophilic amines and alcohols β-hydroxyamide and β-hydroxyester products are generated with enhanced diastereocontrol (up to >95 : 5 dr). Control experiments show that stereoconvergence is observed in the ring-opening of diastereoisomeric β-lactones, leading to a single product (>95 : 5 dr, >99 : 1 er). Mechanistic studies and DFT analysis indicate a substrate controlled Dynamic Kinetic Asymmetric Transformation (DyKAT) involving epimerisation at C(3) of the β-lactone under the reaction conditions, coupled with a hydrogen bond-assisted nucleophilic addition to the Si-face of the β-lactone and stereodetermining ring-opening. The scope and limitations of a one-pot protocol consisting of isothiourea-catalysed enantio-determining [2 + 2] cycloaddition followed by diastereo-determining ring-opening are subsequently developed. Variation within the anhydride ammonium enolate precursor, as well as N(1) and C(3) within the pyrazol-4,5-dione scaffold is demonstrated, giving a range of functionalised β-hydroxyamides with high diastereo- and enantiocontrol (>20 examples, up to >95 : 5 dr and >99 : 1 er) via this DyKAT.