The Most Common Functional Groups in Bioactive Molecules and How Their Popularity Has Evolved over Time

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

Building Block-Centric Approach to DNA-Encoded Library Design

DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.

Unveiling dynamics of nitrogen content and selected nitrogen heterocycles in thrombin inhibitors: a ceteris paribus approach

BACKGROUND

Despite the progress in comprehending molecular design principles and biochemical processes associated with thrombin inhibition, there is a crucial need to optimize efforts and curtail the recurrence of synthesis-testing cycles. Nitrogen and N-heterocycles are key features of many anti-thrombin drugs. Hence, a pragmatic analysis of nitrogen and N-heterocycles in thrombin inhibitors is important throughout the drug discovery pipeline. In the present work, the authors present an analysis with a specific focus on understanding the occurrence and distribution of nitrogen and selected N-heterocycles in the realm of thrombin inhibitors.

RESEARCH DESIGN AND METHODS

A dataset comprising 4359 thrombin inhibitors is used to scrutinize various categories of nitrogen atoms such as ring, non-ring, aromatic, and non-aromatic. In addition, selected aromatic and aliphatic N-heterocycles have been analyzed.

RESULTS

The analysis indicates that ~62% of thrombin inhibitors possess five or fewer nitrogen atoms. Substituted N-heterocycles have a high occurrence, like pyrrolidine (23.24%), pyridine (20.56%), piperidine (16.10%), thiazole (9.61%), imidazole (7.36%), etc. in thrombin inhibitors.

CONCLUSIONS

The majority of active thrombin inhibitors contain nitrogen atoms close to 5 and a combination of N-heterocycles like pyrrolidine, pyridine, piperidine, etc. This analysis provides crucial insights to optimize the transformation of lead compounds into potential anti-thrombin inhibitors.

Electrochemical Dehydration of Dicarboxylic Acids to Their Cyclic Anhydrides

An intramolecular electrochemical dehydration reaction of dicarboxylic acids to their cyclic anhydrides is presented. This electrolysis allows dicarboxylic acids as naturally abundant, inexpensive, safe, and readily available starting materials to be transformed into carboxylic anhydrides under mild reaction conditions. No conventional dehydration reagent is required. The obtained cyclic anhydrides are highly valuable reagents in organic synthesis, and in this report, we use them in-situ for acylation reactions of amines to synthesize amides. This work is part of the recent progress in electrochemical dehydration, which - in contrast to electrochemical dehydrogenative reactions for example - is an underexplored field of research. The reaction mechanism was investigated by 18O isotope labeling, revealing the formation of sulfate by electrochemical oxidation and hydrolysis of the thiocyanate-supporting electrolyte. This transformation is not a classical Kolbe electrolysis, because it is non-decarboxylative, and all carbon atoms of the carboxylic acid starting material are contained in the carboxylic anhydride. In total, 20 examples are shown with NMR yields up to 71 %.

Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning

Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality or even correcting the structure of biomacromolecules. However, vast computational costs and complex quantum mechanics/molecular mechanics (QM/MM) setups limit QR applications. Here we incorporate robust machine learning potentials (MLPs) in multiscale ONIOM(QM:MM) schemes to describe the core parts (e.g., drugs/inhibitors), replacing the expensive QM method. Additionally, two levels of MLPs are combined for the first time to overcome MLP limitations. Our unique MLPs+ONIOM-based QR methods achieve QM-level accuracy with significantly higher efficiency. Furthermore, our refinements provide computational evidence for the existence of bonded and nonbonded forms of the Food and Drug Administration (FDA)-approved drug nirmatrelvir in one SARS-CoV-2 main protease structure. This study highlights that powerful MLPs accelerate QRs for reliable protein-drug complexes, promote broader QR applications and provide more atomistic insights into drug development.

MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations

Combination therapy is a promising strategy for the successful treatment of cancer. The large number of possible combinations, however, mean that it is laborious and expensive to screen for synergistic drug combinations in vitro. Nevertheless, because of the availability of high-throughput screening data and advances in computational techniques, deep learning (DL) can be a useful tool for the prediction of synergistic drug combinations. In this study, we proposed a multimodal DL framework, MMSyn, for the prediction of synergistic drug combinations. First, features embedded in the drug molecules were extracted: structure, fingerprint, and string encoding. Then, gene expression data, DNA copy number, and pathway activity were used to describe cancer cell lines. Finally, these processed features were integrated using an attention mechanism and an interaction module and then input into a multilayer perceptron to predict drug synergy. Experimental results showed that our method outperformed five state-of-the-art DL methods and three traditional machine learning models for drug combination prediction. We verified that MMSyn achieved superior performance in stratified cross-validation settings using both the drug combination and cell line data. Moreover, we performed a set of ablation experiments to illustrate the effectiveness of each component and the efficacy of our model. In addition, our visual representation and case studies further confirmed the effectiveness of our model. All results showed that MMSyn can be used as a powerful tool for the prediction of synergistic drug combinations.

Direct C-H Sulfuration: Synthesis of Disulfides, Dithiocarbamates, Xanthates, Thiocarbamates and Thiocarbonates

In light of the important biological activities and widespread applications of organic disulfides, dithiocarbamates, xanthates, thiocarbamates and thiocarbonates, the continual persuit of efficient methods for their synthesis remains crucial. Traditionally, the preparation of such compounds heavily relied on intricate multi-step syntheses and the use of highly prefunctionalized starting materials. Over the past two decades, the direct sulfuration of C-H bonds has evolved into a straightforward, atom- and step-economical method for the preparation of organosulfur compounds. This review aims to provide an up-to-date discussion on direct C-H disulfuration, dithiocarbamation, xanthylation, thiocarbamation and thiocarbonation, with a special focus on describing scopes and mechanistic aspects. Moreover, the synthetic limitations and applications of some of these methodologies, along with the key unsolved challenges to be addressed in the future are also discussed. The majority of examples covered in this review are accomplished via metal-free, photochemical or electrochemical approaches, which are in alignment with the overraching objectives of green and sustainable chemistry. This comprehensive review aims to consolidate recent advancements, providing valuable insights into the dynamic landscape of efficient and sustainable synthetic strategies for these crucial classes of organosulfur compounds.

Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection

The EU-OPENSCREEN (EU-OS) European Research Infrastructure Consortium (ERIC) is a multinational, not-for-profit initiative that integrates high-capacity screening platforms and chemistry groups across Europe to facilitate research in chemical biology and early drug discovery. Over the years, the EU-OS has assembled a high-throughput screening compound collection, the European Chemical Biology Library (ECBL), that contains approximately 100 000 commercially available small molecules and a growing number of thousands of academic compounds crowdsourced through our network of European and non-European chemists. As an extension of the ECBL, here we describe the computational design, quality control and use case screenings of the European Fragment Screening Library (EFSL) composed of 1056 mini and small chemical fragments selected from a substructure analysis of the ECBL. Access to the EFSL is open to researchers from both academia and industry. Using EFSL, eight fragment screening campaigns using different structural and biophysical methods have successfully identified fragment hits in the last two years. As one of the highlighted projects for antibiotics, we describe the screening by Bio-Layer Interferometry (BLI) of the EFSL, the identification of a 35 μM fragment hit targeting the beta-ketoacyl-ACP synthase 2 (FabF), its binding confirmation to the protein by X-ray crystallography (PDB 8PJ0), its subsequent rapid exploration of its surrounding chemical space through hit-picking of ECBL compounds that contain the fragment hit as a core substructure, and the final binding confirmation of two follow-up hits by X-ray crystallography (PDB 8R0I and 8R1V).

Iodide-umpolung catalytic system for non-traditional amide coupling from nitroalkanes and amines

An N-iodosuccinimide (NIS) catalyst was developed for use in the non-traditional synthesis of amide derivatives from nitroalkanes and amines. In contrast to traditional oxidative catalysis, this catalytic system involves reversing the polarities of two catalytic components (umpolung) by means of a hypervalent iodine reagent. A variety of functional groups were tolerated in the reaction, suggesting that they have the potential for use in other types of oxidative catalytic reactions.

Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations

Relative binding free energy (RBFE) calculations have emerged as a powerful tool that supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular, the setup of such calculations. Atom mapping algorithms are an essential component in setting up automatic large-scale hybrid-topology RBFE calculation campaigns. Traditional algorithms typically employ a 2D subgraph isomorphism solver (SIS) in order to estimate the maximum common substructure. SIS-based approaches can be limited by time-intensive operations and issues with capturing geometry-linked chemical properties, potentially leading to suboptimal solutions. To overcome these limitations, we have developed Kartograf, a geometric-graph-based algorithm that uses primarily the 3D coordinates of atoms to find a mapping between two ligands. In free energy approaches, the ligand conformations are usually derived from docking or other previous modeling approaches, giving the coordinates a certain importance. By considering the spatial relationships between atoms related to the molecule coordinates, our algorithm bypasses the computationally complex subgraph matching of SIS-based approaches and reduces the problem to a much simpler bipartite graph matching problem. Moreover, Kartograf effectively circumvents typical mapping issues induced by molecule symmetry and stereoisomerism, making it a more robust approach for atom mapping from a geometric perspective. To validate our method, we calculated mappings with our novel approach using a diverse set of small molecules and used the mappings in relative hydration and binding free energy calculations. The comparison with two SIS-based algorithms showed that Kartograf offers a fast alternative approach. The code for Kartograf is freely available on GitHub (https://github.com/OpenFreeEnergy/kartograf). While developed for the OpenFE ecosystem, Kartograf can also be utilized as a standalone Python package.

Photocatalytic Sulfonyl Peroxidation of Alkenes via Deamination of N-Sulfonyl Ketimines

A photocatalytic three-component sulfonyl peroxidation of alkenes with N-sulfonyl ketimines and tert-butyl hydroperoxide is reported. The reaction takes place via the photoinduced EnT process, which allows the efficient synthesis of a variety of β-peroxyl sulfones under mild reaction conditions in the absence of a transition metal catalyst. The downstream derivatizations of the peroxides were also performed. Furthermore, the utility of this protocol was manifested by the synthesis of 11β-HSD1 inhibitor and the antiprostate cancer drug bicalutamide.

At the Speed of Light: The Systematic Implementation of Photoredox Cross-Coupling Reactions for Medicinal Chemistry Research

The adoption of new and emerging techniques in organic synthesis is essential to promote innovation in drug discovery. In this Perspective, we detail the strategy we used for the systematic deployment of photoredox-mediated, metal-catalyzed cross-coupling reactions in AbbVie's medicinal chemistry organization, focusing on topics such as assessment, evaluation, implementation, and accessibility. The comprehensive evaluation of photoredox reaction setups and published methods will be discussed, along with internal efforts to build expertise and photoredox high-throughput experimentation capabilities. We also highlight AbbVie's academic-industry collaborations in this field that have been leveraged to develop new synthetic strategies, along with discussing the internal adoption of photoredox cross-coupling reactions. The work described herein has culminated in robust photocatalysis and cross-coupling capabilities which are viewed as key platforms for medicinal chemistry research at AbbVie.

Photoredox-Catalyzed Preparation of Sulfones Using Bis-Piperidine Sulfur Dioxide - An Underutilized Reagent for SO2 Transfer

Sulfonyl groups are widely observed in biologically relevant molecules and consequently, SO2 capture is an increasingly attractive method to prepare these sulfonyl-containing compounds given the range of SO2 -surrogates now available as alternatives to using the neat gas. This, along with the advent of photoredox catalysis, has enabled mild radical capture of SO2 to emerge as an effective route to sulfonyl compounds. Here we report a photoredox-catalyzed cross-electrophile sulfonylation of aryl and alkyl bromides making use of a previously under-used amine-SO2 surrogate; bis(piperidine) sulfur dioxide (PIPSO). A broad selection of alkyl and aryl bromides were photocatalytically converted to their corresponding sulfinates and then trapped with various electrophiles in a one-pot multistep procedure to prepare sulfones and sulfonamides.

Palladium-Catalyzed Carbonylative Multicomponent Fluoroalkylation of 1,3-Enynes: Concise Construction of Diverse Cyclic Compounds

Multicomponent reactions, particularly those entailing four or more reagents, have presented a longstanding challenge due to the inherent complexities associated with balancing reactivity, selectivity, and compatibility. In this study, we describe a palladium-catalyzed multi-component fluoroalkylative carbonylation of 1,3-enynes. A series of products featuring three active functional groups-allene, fluoroalkyl, and carboxyl, were efficiently and selectively integrated in a single chemical operation. Furthermore, more intricate fluoroalkyl-substituted pyrimidinones can be constructed by simply altering the 1,3-bisnucleophilic reagent. This approach also provides a valuable strategy for the late-stage modification of naturally occurring molecules and concise construction of diverse cyclic compounds.

Expanded Access to Fluoroformamidines via a Modular Synthetic Pathway

Fluoroformamidines are an underutilized and understudied functional group despite combining two of the most highly prized elements in drug design: nitrogen and fluorine. We report a practical and modular synthesis of fluoroformamidines via the rearrangement of in situ-generated amidoximes. High yields in just 60 s at room temperature highlight the efficiency of this protocol. Furthermore, fluoroformamidines proved to be useful intermediates in the synthesis of diverse ureas and carbamimidates.

Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning

We present a quantum mechanical/machine learning (ML) framework based on random forest to accurately predict the pKas of complex organic molecules using inexpensive density functional theory (DFT) calculations. By including physics-based features from low-level DFT calculations and structural features from our connectivity-based hierarchy (CBH) fragmentation protocol, we can correct the systematic error associated with DFT. The generalizability and performance of our model are evaluated on two benchmark sets (SAMPL6 and Novartis). We believe the carefully curated input of physics-based features lessens the model's data dependence and need for complex deep learning architectures, without compromising the accuracy of the test sets. As a point of novelty, our work extends the applicability of CBH, employing it for the generation of viable molecular descriptors for ML.

Synthetic derivatives of natural cinnamic acids as potential anti-colorectal cancer agents

Cinnamic acid and its derivatives represent attractive building blocks for the development of pharmacological tools. A series of piperoniloyl and cinnamoyl-based amides (6-9 a-f) have been synthesized and assayed against a wide panel of colorectal cancer (CRC) cells, with the aim of finding promising anticancer agents. Among all twenty-four synthesized molecules, 7a, 7e-f, 9c, and 9f displayed the best antiproliferative activity. The induced G1 cell cycle arrest and the increase in apoptotic cell death was seen in FACS analysis and western Blotting in the colon tumor cell lines HCT116, SW480, LoVo, and HT29, but not in the nontumor cell line HCEC. In particular, 9f overcame the resistance of HT29 cells, which have a mutant p53 and BRAF. Furthermore, 9f, amide of piperonilic acid with the 3,4-dichlorobenzyl substituent upregulated p21, which is involved in cell cycle arrest as well as in apoptosis induction. Cinnamic acid derivatives might be potential anticancer compounds, useful for the development of promising anti-CRC agents.

Leveraging nitrogen occurrence in approved drugs to identify structural patterns

BACKGROUND

The process of drug development and discovery is costly and slow. Although an understanding of molecular design principles and biochemical processes has progressed, it is essential to minimize synthesis-testing cycles. An effective approach is to analyze key heteroatoms, including oxygen and nitrogen. Herein, we present an analysis focusing on the utilization of nitrogen atoms in approved drugs.

RESEARCH DESIGN AND METHODS

The present work examines the frequency, distribution, prevalence, and diversity of nitrogen atoms in a dataset comprising 2,049 small molecules approved by different regulatory agencies (FDA and others). Various types of nitrogen atoms, such as sp3-, sp2-, sp-hybridized, planar, ring, and non-ring are included in this investigation.

RESULTS

The results unveil both previously reported and newly discovered patterns of nitrogen atom distribution around the center of mass in the majority of drug molecules.

CONCLUSIONS

This study has highlighted intriguing trends in the role of nitrogen atoms in drug design and development. The majority of drugs contain 1-3 nitrogen atoms within 5Å from the center of mass (COM) of a molecule, with a higher preference for the ring and planar nitrogen atoms. The results offer invaluable guidance for the multiparameter optimization process, thus significantly contributing toward the conversion of lead compounds into potential drug candidates.

Formation of C-B, C-C, and C-X Bonds from Nonstabilized Aryl Radicals Generated from Diaryl Boryl Radicals

With the development of organoboron chemistry, boron-centered radicals have become increasingly attractive. However, their synthetic applications remain limited in that they have been used only as substrates for addition reactions or as initiators for catalytic reactions. We have achieved a new reaction pathway in which tetraarylborate salts are used as precursors for aryl radicals via boron radicals, by introducing a simple activation reagent. In addition, we carried out a diverse array of transformations involving these aryl radical precursors, which allowed the construction of new C-B, C-C, and C-X bonds in the presence of visible light.

Chemoselective α-Trifluoroacetylation of Amides Using Highly Electrophilic Trifluoroacetic Anhydrides and 2,4,6-Collidine

Chemoselective α-acylation of tertiary amides proceeded with highly electrophilic acid anhydrides and weak bases under mild conditions. β-Ketoamides containing trifluoroacetyl or perfluoroacyl groups were selectively obtained even in the presence of other functional groups such as ketone, ester, etc. Density functional theory calculations suggest that 1-acyloxyenamine is the key intermediate for the chemoselective α-acylation.

Secondary-sphere preorganization enables nickel-catalyzed nitrile hydroboration

Herein, we describe nickel-catalyzed nitrile hydroboration with pinacolborane, wherein a tethered NHC-pyridonate ligand enables efficient catalysis (5 mol% [Ni], ≤6 h reaction time) at room temperature. Mechanistic studies, including isolation of the catalytically relevant intermediates, shed light on the cooperative role of the ligand in activating both reagents simultaneously.

An Acid-Controlled Method for the Regioselective Functionalization of Anilines over Aliphatic Amines

Regioselective transformations at similar functional groups are of paramount importance in organic synthesis. Traditional strategies towards regioselective functionalization include serial protection/deprotection and sequential synthesis. Modern organic synthesis emphasizes pathway efficiency and protecting group free routes with a goal of exploiting inherent differences in reactivity. This study reports a method for the regioselective functionalization of anilines over aliphatic amines. Utilizing classic conditions for the Baeyer-Mills reaction, anilines were shown to react preferentially in the presence of aliphatic amines. Subsequently, this principle of reactivity was extended to other electrophiles and conditions.

Expanding the Role of Boron in New Drug Chemotypes: Properties, Chemistry, Pharmaceutical Potential of Hemiboronic Naphthoids

New chemotypes and bioisosteres can open a new chemical space in drug discovery and help meet an urgent demand for novel agents to fight infections and other diseases. With the aim of identifying new boron-containing drug chemotypes, this article details a comprehensive evaluation of the pseudoaromatic hemiboronic naphthoids, benzoxaza- and benzodiazaborines. Relevant physical properties in aqueous media (acidity, solubility, log P, and stability) of prototypic members of four subclasses were determined. Both scaffolds are amenable to common reactions used in drug discovery, such as chemoselective Suzuki-Miyaura, Chan-Lam, and amidation reactions. Small model libraries were prepared to assess the scope of these transformations, and the entire collection was screened for antifungal (Candida albicans) and antibacterial activity (MRSA, Escherichia coli), unveiling promising benzoxazaborines with low micromolar minimum inhibitory concentration values. Select DMPK assays of representative compounds suggest promising drug-like behavior for all four subclasses. Moreover, several drug isosteres were evaluated for anti-inflammatory and anticancer activity as appropriate.

1,2-Redox Transpositions of Tertiary Amides

Reactions capable of transposing the oxidation levels of adjacent carbon atoms enable rapid and fundamental alteration of a molecule's reactivity. Herein, we report the 1,2-transposition of the carbon atom oxidation level in cyclic and acyclic tertiary amides, resulting in the one-pot synthesis of 1,2- and 1,3-oxygenated tertiary amines. This oxidation level transfer was facilitated by the careful orchestration of an iridium-catalyzed reduction with the functionalization of transiently formed enamine intermediates. A novel 1,2-carbonyl transposition is described, and the breadth of this redox transposition strategy has been further explored by the development of aminoalcohol and enaminone syntheses. The diverse β-functionalized amine products were shown to be multifaceted and valuable synthetic intermediates, accessing challenging biologically relevant motifs.

Biocatalysis in Drug Design: Engineered Reductive Aminases (RedAms) Are Used to Access Chiral Building Blocks with Multiple Stereocenters

Novel building blocks are in constant demand during the search for innovative bioactive small molecule therapeutics by enabling the construction of structure-activity-property-toxicology relationships. Complex chiral molecules containing multiple stereocenters are an important component in compound library expansion but can be difficult to access by traditional organic synthesis. Herein, we report a biocatalytic process to access a specific diastereomer of a chiral amine building block used in drug discovery. A reductive aminase (RedAm) was engineered following a structure-guided mutagenesis strategy to produce the desired isomer. The engineered RedAm (IR-09 W204R) was able to generate the (S,S,S)-isomer 3 in 45% conversion and 95% ee from the racemic ketone 2. Subsequent palladium-catalyzed deallylation of 3 yielded the target primary amine 4 in a 73% yield. This engineered biocatalyst was used at preparative scale and represents a potential starting point for further engineering and process development.

Regioselective and Enantioselective Copper-Catalyzed Hydroaminocarbonylation of Unactivated Alkenes and Alkynes

Given the prevalence of amide backbones in marketed pharmaceuticals and their ubiquity as critical binding units in natural peptides and proteins, it remains important to develop novel methods to construct amide bonds. We report here a general method for the anti-Markovnikov hydroaminocarbonylation of unactivated alkenes under mild conditions, using copper catalysis in combination with hydroxylamine electrophile reagents and poly(methylhydrosiloxane) (PMHS) as a cheap and environmentally friendly hydride source. The reaction tolerates a variety of functional groups and efficiently converts unactivated terminal alkenes, 1,1-disubstituted alkenes, and cyclic alkenes to the corresponding amides with exclusive anti-Markovnikov selectivity (and high enantioselectivities/diastereoselectivities). Additionally, with minimal modification of the reaction conditions, alkynes can also undergo tandem hydrogenation-hydroaminocarbonylation to alkyl amides.

Green metrics in mechanochemistry

The development of new green methodologies and their broader adoption for promoting sustainable development in chemistry laboratories and industry play a significant role in society, due to the economic importance of chemistry and its widespread presence in everyday life. Therefore, a sustainable approach to chemistry contributes to the well-being of the worldwide population and complies with the United Nations Sustainable Development Goals (UN SDGs) and the European Green Deal. The review highlights how batch and continuous mechanochemical methods are an eco-friendly approach for organic synthesis, with a lower environmental footprint in most cases, compared to solution-based procedures. The assessment is objectively based on the use of green metrics (e.g., atom and real atom economy, E-factor, process mass intensity, material parameter recovery, Eco-scale, stoichiometric factor, etc.) and indicators (e.g. DOZN tool and life cycle assessment, LCA, studies) applied to organic transformations such as synthesis of the amide bond, carbamates, heterocycles, active pharmaceutical ingredients (APIs), porphyrins, porous organic polymers (POPs), metal- or acid-catalysed processes, multicomponent and condensation reactions, rearrangements, etc. The generalized absence of bulk solvents, the precise control over the stoichiometry (i.e., using agents in a stoichiometrically rather than in excess), and the more selective reactions enabling simplified work-up procedures are the distinctive factors, marking the superiority of mechanochemical processes over solution-based chemistry.

Hydrogenative alkene perdeuteration aided by a transient cooperative ligand

Deuterogenation of unsaturated organic compounds is an attractive route for installing C(sp3)-D bonds, but the existing methods typically use expensive D2 and introduce only two deuterium atoms per unsaturation. Herein we report the hydrogenative perdeuteration of alkenes using readily available H2 and D2O instead of D2, catalysed by an acridanide-based ruthenium pincer complex and resulting in the incorporation of up to 4.9 D atoms per C=C double bond in a single synthetic step. Importantly, adding a catalytic amount of thiol, which serves as a transient cooperative ligand, ensures the incorporation of deuterium rather than protium by balancing the rates of two sequential deuteration processes. The current method opens an avenue for installing perdeuteroalkyl groups at specific sites from widely available alkenes under mild conditions.

Distinguishing Competing Mechanistic Manifolds for C(acyl)-N Functionalization by a Ni/N-Heterocyclic Carbene Catalyst System

Carboxylic acid derivatives are appealing alternatives to organohalides as cross-coupling electrophiles for fine chemical synthesis due to their prevalence in biomass and bioactive small molecules as well as their ease of preparation and handling. Within this family, carboxamides comprise a versatile electrophile class for nickel-catalyzed coupling with carbon and heteroatom nucleophiles. However, even state-of-the-art C(acyl)-N functionalization and cross-coupling reactions typically require high catalyst loadings and specific substitution patterns. These challenges have proven difficult to overcome, in large part due to limited experimental mechanistic insight. In this work, we describe a detailed mechanistic case study of acylative coupling reactions catalyzed by the commonly employed Ni/SIPr catalyst system (SIPr = 1,3-bis(2,6-di-isopropylphenyl)-4,5-dihydroimidazol-2-ylidine). Stoichiometric organometallic studies, in situ spectroscopic measurements, and crossover experiments demonstrate the accessibility of Ni(0), Ni(I), and Ni(II) resting states. Although in situ precatalyst activation limits reaction efficiency, the low concentrations of active, SIPr-supported Ni(0) select for electrophile-first (closed-shell) over competing nucleophile-first (open-shell) mechanistic manifolds. We anticipate that the experimental insights into the nature and controlling features of these distinct pathways will accelerate rational improvements to cross-coupling methodologies involving pervasive carboxamide substrate motifs.

FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction

Artificial intelligence-based molecular property prediction plays a key role in molecular design such as bioactive molecules and functional materials. In this study, we propose a self-supervised pretraining deep learning (DL) framework, called functional group bidirectional encoder representations from transformers (FG-BERT), pertained based on ~1.45 million unlabeled drug-like molecules, to learn meaningful representation of molecules from function groups. The pretrained FG-BERT framework can be fine-tuned to predict molecular properties. Compared to state-of-the-art (SOTA) machine learning and DL methods, we demonstrate the high performance of FG-BERT in evaluating molecular properties in tasks involving physical chemistry, biophysics and physiology across 44 benchmark datasets. In addition, FG-BERT utilizes attention mechanisms to focus on FG features that are critical to the target properties, thereby providing excellent interpretability for downstream training tasks. Collectively, FG-BERT does not require any artificially crafted features as input and has excellent interpretability, providing an out-of-the-box framework for developing SOTA models for a variety of molecule (especially for drug) discovery tasks.

The isocyanide SN2 reaction

The SN2 nucleophilic substitution reaction is a vital organic transformation used for drug and natural product synthesis. Nucleophiles like cyanide, oxygen, nitrogen, sulfur, or phosphorous replace halogens or sulfonyl esters, forming new bonds. Isocyanides exhibit unique C-centered lone pair σ and π* orbitals, enabling diverse radical and multicomponent reactions. Despite this, their nucleophilic potential in SN2 reactions remains unexplored. We have uncovered that isocyanides act as versatile nucleophiles in SN2 reactions with alkyl halides. This yields highly substituted secondary amides through in situ nitrilium ion hydrolysis introducing an alternative bond break compared to classical amide synthesis. This novel 3-component process accommodates various isocyanide and electrophile structures, functional groups, scalability, late-stage drug modifications, and complex compound synthesis. This reaction greatly expands chemical diversity, nearly doubling the classical amid coupling's chemical space. Notably, the isocyanide nucleophile presents an unconventional Umpolung amide carbanion synthon (R-NHC(-) = O), an alternative to classical amide couplings.

Synthesis of 1-Methylcyclopropyl Aryl Ethers from Phenols Using an Alkenylation-Cyclopropanation Sequence

1-Methylcyclopropyl aryl ethers (McPAEs) can be viewed as cyclized derivatives of their O-tert-butyl counterparts. Although these compounds can find use in medicinal chemistry, they are much less represented in the literature than their aryl cyclopropyl ether analogues. McPAEs are generally prepared via an SNAr reaction using 1-methylcyclopropanol. However, this method works exclusively with highly deactivated arenes. We report herein a two-step sequence to access McPAEs consisting of the 1-methylvinylation of phenols followed by cyclopropanation of the corresponding 1-methylvinyl aryl ethers. Isomeric mono- and dimethyl analogues were also prepared using this sequence.

Modern Strategies for Carbon Isotope Exchange

In contrast to stable and natural abundant carbon-12, the synthesis of organic molecules with carbon (radio)isotopes must be conceived and optimized in order to navigate through the hurdles of radiochemical requirements, such as high costs of the starting materials, harsh conditions and radioactive waste generation. In addition, it must initiate from the small cohort of available C-labeled building blocks. For long time, multi-step approaches have represented the sole available patterns. On the other side, the development of chemical reactions based on the reversible cleavage of C-C bonds might offer new opportunities and reshape retrosynthetic analysis in radiosynthesis. This review aims to provide a short survey on the recently emerged carbon isotope exchange technologies that provide effective opportunity for late-stage labeling. At present, such strategies have relied on the use of primary and easily accessible radiolabeled C1-building blocks, such as carbon dioxide, carbon monoxide and cyanides, while the activation principles have been based on thermal, photocatalytic, metal-catalyzed and biocatalytic processes.

Preparation of medicinally active extracts and phytochemical characterisation of phytoconstituents from medicinal plants

Medicinal plants contain many bioactive compounds that are often hosted in medicinally active extracts generated from their various parts. The quest for reliable products from medicinal plants escalated in recent years as an answer to emerging health complications and the much-needed sufficient scientific backing that is dependent on proper preparation and characterisation principles of active extracts. This study described the Soxhlet and the maceration methods that are used to process extracts from the inert materials of medicinal plants using appropriate biocompatible solvents, the phytochemical screening assays, and TLC, UV spectrometry, FT-IR, and GC-MS techniques used in phytochemical studies. These techniques are crucial in studies that are meant to explore the active components of medicinal plants and their relative pharmacological effects. This information can be used as a guide when formulating effective yet less toxic plant-derived drugs and provide opportunities to upgrade while reducing further complexity in phytochemical studies.

Low Pressure Carbonylation of Benzyl Carbonates and Carbamates for Applications in 13 C Isotope Labeling and Catalytic CO2 Reduction

Herein, we report a methodology to access isotopically labeled esters and amides from carbonates and carbamates employing an oxygen deletion strategy. This methodology utilizes a decarboxylative carbonylation approach for isotope labeling with near stoichiometric, ex situ generated 12 C, or 13 C carbon monoxide. This reaction is characterized by its broad scope, functional group tolerance, and high yields, which is showcased with the synthesis of structurally complex molecules. A complementary method that operates by the catalytic in situ generation of CO via the reduction of CO2 liberated during decarboxylation has also been developed as a proof-of-concept approach that CO2 -derived compounds can be converted to CO-containing frameworks. Mechanistic studies provide insight into the catalytic steps which highlight the impact of ligand choice to overcome challenges associated with low-pressure carbonylation methodologies, along with rational for the development of future methodologies.

Visible-light-mediated sulfonylation of anilines with sulfonyl fluorides

Sulfonylaniline motif plays an important role in pharmaceutical sciences. Developed methods towards this structure are typically lack of good modifiability and stability. In this study, visible-light-mediated sulfonylation of aniline using sulfonyl fluoride as a modifiable and stable sulfonylation reagent is described. A variety of substituted sulfonylanilines were synthesized under mild reaction conditions with moderate to good efficiency. The example of late-stage sulfonylation highlighted the advantage of using sulfonyl fluoride as a sulfonylation reagent. In addition, the crucial influence of counterions on the photocatalyst observed in this system would inspire further research on the photochemistry of sulfonyl fluoride.

Intermolecular Metal-Catalyzed C‒C Coupling of Unactivated Alcohols or Aldehydes for Convergent Ketone Construction beyond Premetalated Reagents

Intermolecular metal-catalyzed C‒C couplings of unactivated primary alcohols or aldehydes to form ketones are catalogued. Reactions are classified on the basis of pronucleophile. Protocols involving premetalated reagents or reactants that incorporate directing groups are not covered. These methods represent an emerging alternative to classical multi-step protocols for ketone construction that exploit premetalated reagents, and/or steps devoted to redox manipulations and carboxylic acid derivatization.

Chemoselective N-Acylation of Amines with Acylsilanes under Aqueous Acidic Conditions

We report a facile method for forming amide bonds between acylsilanes and a wide range of amines in the presence of a mild chlorinating agent under aqueous acidic conditions. The reaction is highly chemoselective, as exemplified by the late-stage modification of a panel of approved drugs and natural products containing reactive functionalities.

Oxetane Synthesis via Alcohol C-H Functionalization

Oxetanes are strained heterocycles with unique properties that have triggered significant advances in medicinal chemistry. However, their synthesis still presents significant challenges that limit the use of this class of compounds in practical applications. In this Letter, we present a methodology that introduces a new synthetic disconnection to access oxetanes from native alcohol substrates. The generality of the approach is demonstrated by the application in late-stage functionalization chemistry, which is further exploited to develop a single-step synthesis of a known bioactive synthetic steroid derivative that previously required at least four synthetic steps from available precursors.

Reductive Arylation of Nitroarenes with Chloroarenes: Reducing Conditions Enable New Reactivity from Palladium Catalysts

Palladium-catalyzed C-N bond forming reactions are a key tool in modern synthetic organic chemistry. Despite advances in catalyst design enabling the use of a variety of aryl (pseudo)halides, the necessary aniline coupling partner is often synthesized in a discrete reduction step from a nitroarene. An ideal synthetic sequence would avoid the necessity of this step while maintaining the reliable reactivity of palladium catalysis. Herein, we describe how reducing conditions enable new chemical steps and reactivity from well-studied palladium catalysts, resulting in a new, useful transformation: the reductive arylation of nitroarenes with chloroarenes to form diarylamines. Mechanistic experiments suggest that under reducing conditions, BrettPhos-palladium complexes catalyze the dual N-arylation of typically inert azoarenes─generated via the in situ reduction of nitroarenes─via two distinct mechanisms. Initial N-arylation proceeds via a novel association-reductive palladation sequence followed by reductive elimination to yield an intermediate 1,1,2-triarylhydrazine. Arylation of this intermediate by the same catalyst via a traditional amine arylation sequence forms a transient tetraarylhydrazine, unlocking reductive N-N bond cleavage to liberate the desired product. The resulting reaction allows for the synthesis of diarylamines bearing a variety of synthetically valuable functionalities and heteroaryl cores in high yield.

Chitosan-Based Hydrogel in the Management of Dermal Infections: A Review

The main objective of this review is to provide a comprehensive overview of the current evidence regarding the use of chitosan-based hydrogels to manage skin infections. Chitosan, a naturally occurring polysaccharide derived from chitin, possesses inherent antimicrobial properties, making it a promising candidate for treating various dermal infections. This review follows a systematic approach to analyze relevant studies that have investigated the effectiveness of chitosan-based hydrogels in the context of dermal infections. By examining the available evidence, this review aims to evaluate these hydrogels' overall efficacy, safety, and potential applications for managing dermal infections. This review's primary focus is to gather and analyze data from different recent studies about chitosan-based hydrogels combating dermal infections; this includes assessing their ability to inhibit the growth of microorganisms and reduce infection-related symptoms. Furthermore, this review also considers the safety profile of chitosan-based hydrogels, examining any potential adverse effects associated with their use. This evaluation is crucial to ensure that these hydrogels can be safely utilized in the management of dermal infections without causing harm to patients. The review aims to provide healthcare professionals and researchers with a comprehensive understanding of the current evidence regarding the use of chitosan-based hydrogels for dermal infection management. The findings from this review can contribute to informed decision-making and the development of potential treatment strategies in this field.

Nms-Amides: An Amine Protecting Group with Unique Stability and Selectivity

p-Toluenesulfonyl (Tosyl) and nitrobenzenesulfonyl (Nosyl) are two of the most common sulfonyl protecting groups for amines in contemporary organic synthesis. While p-toluenesulfonamides are known for their high stability/robustness, their use in multistep synthesis is plagued by difficult removal. Nitrobenzenesulfonamides, on the other hand, are easily cleaved but display limited stability to various reaction conditions. In an effort to resolve this predicament, we herein present a new sulfonamide protecting group, which we term Nms. Initially developed through in silico studies, Nms-amides overcome these previous limitations and leave no room for compromise. We have investigated the incorporation, robustness and cleavability of this group and found it to be superior to traditional sulfonamide protecting groups in a broad range of case studies.

An Electrochemical Design for Catalytic Dehydration: Direct, Room-Temperature Esterification without Acid or Base Additives

An electrochemical approach has been leveraged to underpin a new conceptual platform for dehydration reactions, which has been demonstrated in the context of esterification. Esters were prepared from the corresponding acid and alcohol partners at room temperature without acid or base additives and without consuming stoichiometric reagents. This methodology therefore addresses key complications that plague esterification and dehydration reactions more broadly and that represent a leading challenge in synthetic chemistry.

Visible-Light/Nickel-Catalyzed Carboxylation of C(sp2) Bromides via Formate Activation

A new visible-light-driven method for the carboxylation of (hetero)aryl/vinyl bromides has been developed using catalytic 4CzIPN, nickel, phenyl triflimide, and sodium formate as a carboxylation agent. Interestingly, we found catalytic phenyl triflimide plays an essential role in promoting the reaction. While many C(sp²) carboxylation reactions require harsh reagents or gaseous carbon dioxide, we demonstrate the mild and facile construction of carboxylic acids from readily available starting materials.

Direct 18F-Fluorosulfurylation of Phenols and Amines Using an [18F]FSO2+ Transfer Agent Generated In Situ

We report the direct radiofluorosulfurylation method for the synthesis of ¹⁸F-labeled fluorosulfuryl derivatives from phenols and amines using an [¹⁸F]FSO₂⁺ transfer agent generated in situ. Nucleophilic radiofluorination is achieved even in a hydrous organic medium, obviating the need for azeotropic drying and the use of cryptands. This unprecedented, operationally simple isotopic functionalization facilitates the reliable production of potential radiotracers for positron emission tomography, rendering facile access to SuFEx radiochemistry.

"Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery

Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.

Rapid determination of essential oils functional groups using compositional methods and VisNIR spectroscopy

Essential oils (EOs) are natural products formed by plant volatile compounds. EOs are frequently used in the cosmetic and food industries as well as for domestic purposes, because of their physiochemical, biological and sensory properties. The functional groups (FG), corresponding to various chemical structures present in EOs, are responsible for their biological activities. Therefore, simple, rapid, and economical techniques suitable to characterize the EOs features by measuring their contents, are of great interest. Near-infrared spectroscopy (NIRS) highlights because of its rapidity, and being no-contaminant, as a potential solution. Multivariate correlation methods are commonly used to build NIRS calibrations. These methods were designed for the real space, that is for values comprised between - ∞ and + ∞. However, EOs components are co-dependent data restricted to a simplex space. These are the so-called compositional data (CoDa), needing specific methods to be correlated with a set of spectral explicative variables. In this study, compositional visible and near-infrared (VISNIRS) models have been assessed to quantify the FG of the analyzed EOs. For this purpose, the FG were organized according to their greater frequency in 1) alcohol; 2) ether; 3) ester; 4) aldehydes; 5) ketones, and the hydrocarbon fraction representing the remainder EOs mass, to characterize them. The approach of this study, based on compositional models from VISNIRS spectra, has provided a satisfactory predictive performance for the quantitative estimation of the main FG of the EOs. The proposed approach can be an alternative to traditional chemical methods to characterize EOs.

Rapid Access to Carbon-Isotope-Labeled Alkyl and Aryl Carboxylates Applying Palladacarboxylates

Herein, we report a strategy for the formation of isotopically labeled carboxylic esters from boronic esters/acids using a readily accessible palladium carboxylate complex as an organometallic source of isotopically labeled functional groups. The reaction allows access to either unlabeled or full ¹³C- or ¹⁴C-isotopically labeled carboxylic esters, and the method is characterized by its operational simplicity, mild conditions, and general substrate scope. Our protocol is further extended to a carbon isotope replacement strategy, involving an initial decarbonylative borylation procedure. Such an approach allows access to isotopically labeled compounds directly from the unlabeled pharmaceutical, which can have implications for drug discovery programs.

Identification of new oxospiro chromane quinoline-carboxylate antimalarials that arrest parasite growth at ring stage

Malaria still threatens half the globe population despite successful Artemisinin-based combination therapy. One of the reasons for our inability to eradicate malaria is the emergence of resistance to current antimalarials. Thus, there is a need to develop new antimalarials targeting Plasmodium proteins. The present study reported the design and synthesis of 4, 6 and 7-substituted quinoline-3-carboxylates 9(a-o) and carboxylic acids 10(a-b) for the inhibition of Plasmodium N-Myristoyltransferases (NMTs) using computational biology tools followed by chemical synthesis and functional analysis. The designed compounds exhibited a glide score of -9.241 to -6.960 kcal/mol for PvNMT and -7.538 kcal/mol for PfNMT model proteins. Development of the synthesized compounds was established via NMR, HRMS and single crystal X-ray diffraction study. The synthesized compounds were evaluated for their in vitro antimalarial efficacy against CQ-sensitive Pf3D7 and CQ-resistant PfINDO lines followed by cell toxicity evaluation. In silico results highlighted the compound ethyl 6-methyl-4-(naphthalen-2-yloxy)quinoline-3-carboxylate (9a) as a promising inhibitor with a glide score of -9.084 kcal/mol for PvNMT and -6.975 kcal/mol for PfNMT with IC50 values of 6.58 µM for Pf3D7 line. Furthermore, compounds 9n and 9o exhibited excellent anti-plasmodial activity (Pf3D7 IC50 = 3.96, 6.71 µM, and PfINDO IC50 = 6.38, 2.8 µM, respectively). The conformational stability of 9a with the active site of the target protein was analyzed through MD simulation and was found concordance with in vitro results. Thus, our study provides scaffolds for the development of potent antimalarials targeting both Plasmodium vivax and Plasmodium falciparum.Communicated by Ramaswamy H. Sarma.