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

Synthesis, screening and validation of cysteine-reactive fragments as chikungunya virus protease inhibitors

Alphaviruses like the Chikungunya virus cause severe outbreaks; however, no specific treatments are available. Their viral replication depends on the nsP2 cysteine protease, a promising but underexplored target for drug discovery. In this study, we report a covalent fragment screening against Chikungunya virus nsP2 protease, resulting in the identification of three inhibitors that can serve as starting points for future drug development. Careful validation proved indispensable in eliminating false-positive hits from a Förster resonance energy transfer (FRET)-based inhibition assay, wherein interference was caused by the inner filter effect between the fluorescent substrate and coloured compounds. Jump-dilution experiments accompanied by reactivity studies with cysteine and the recombinant protein indicate covalent inhibition via thia-Michael addition. We further demonstrate cross-inhibition of the related alphavirus nsP2 protease from Sindbis virus. The study provides early insights into nsP2 inhibition by electrophilic fragments featuring non-promiscuous N-arylacrylamides, thus advancing the search for antivirals targeting Chikungunya and other alphaviruses of concern.

Building lactams by highly selective hydrodeoxygenation of cyclic imides using an alumina-supported AgRe bimetallic nanocatalyst

The rational design of robust nanocatalysts containing the suitable active sites for building relevant organic compounds, such as lactams, is a desired approximation towards the development of a sustainable fine chemistry field. In that sense, the design of a proper nanomaterial able to mediate the selective hydrodeoxygenation of cyclic imides to lactams with high tolerance to the preservation of aromatic rings remains rather unexplored. Here, we show the design of a bimetallic AgRe nanomaterial with notable activity and selectivity to mediate this transformation affording more than 60 lactams from the corresponding imides. Interestingly, in this work we disclose that the optimal AgRe nanocatalyst is constituted by AgReO4 nanoaggregates that undergo an in situ hydrogenative dispersion to form the active centers composed by Ag0 nanoparticles and ReOx species. Deep characterization, together with kinetic and mechanistic studies, have revealed that the intimate Ag-Re contact intrinsic to AgReO4 species is key for the formation of the most active catalytic sites and the proper bimetallic cooperation required for mediating the desired process.

Direct synthesis of ethers from alcohols & aldehydes enabled by an oxocarbenium ion interception strategy

A new method has been established for formation of ethers from aldehydes and alcohols - a net reductive etherification. Reactions of these entities with phosphines in the presence of acid enable formation of α-(alkoxyalkyl)phosphonium salts, which, upon hydrolysis, result in formation of ether products in isolated yields of 63-92%. Formation and hydrolysis of the α-(alkoxyalkyl)phosphonium salts were done in an efficient telescoped two-step, one-pot process that does not require inert atmosphere conditions. Formation of the key phosphonium salt intermediates was found to occur in preference to acetal formation and is proposed based on both experimental and computational evidence to involve interception of oxocarbenium ions formed by reaction of the aldehyde, alcohol and acid by phosphine. This method represents the first instance in which net reductive etherifications have been achieved without the requirement for use of hydrides or hydrogen as reductants, and exhibits excellent functional group tolerance, thus enabling facile hydride-free synthesis of ethers. These are amongst the most important functional groups in organic synthesis. The new etherification method also enables deuteride-free synthesis of deuterated ethers.

Radical photochemical difluorosulfoximination of alkenes and propellanes

Herein, we report a metal-free divergent visible-light driven method for the synthesis of fluorinated sulfoximines. Both olefins and propellanes efficiently undergo difluorosulfoximination with yields up to 77% (65 examples). The process is general and robust and tolerates diverse functional groups, including esters, ethers, ketones, silyl groups, silyl ethers or boronic esters. The functionalization of diverse bioactive ingredients (8 examples) and various product manipulations demonstrate the synthetic usefulness of the developed synthetic platform. Finally, we rationalized the divergent reaction mechanism by performing Stern-Volmer quenching and EPR experiments that revealed the key activity of a difluoroalkyl sulfoximine radical.

A Photo- and Electrochemistry-Triggered Redox-Neutral Cyclization Strategy to Access Cyclic N-CF3 Amides

While the construction of N-CF3 amides has seen significant progress, the current synthetic repertoire is largely limited to noncyclic variants. Here, we report synthetic access to N-CF3 isoindolinones. The developed redox-neutral cyclization leverages amino acid-derived N-CF3 redox-active esters under photo- or electrochemical activation. Mechanistic studies reveal that N-CF3 uniquely enables this disconnection through its distinct electronic impact, which enhances conformational flexibility and lowers the propensity for overoxidation.

PCET-mediated deconstructive cross-coupling of aliphatic alcohols

A practical deconstructive arylation of aliphatic alcohols has been developed using a synergistic photoredox proton-coupled electron transfer (PCET) and nickel dual catalytic system. The method efficiently generates alkyl radicals via concerted PCET-mediated β-scission, enabling the formation of C(sp3)-C(sp2) bonds between alcohols and aryl halides. Optimization studies revealed a broad functional group tolerance and high chemoselectivity, with good yields even for challenging tertiary alcohol substrates. Mechanistic insights from transient absorption spectroscopy confirmed the dominance of a PCET pathway for radical generation. This strategy expands the utility of alcohols as alkyl radical precursors in cross-coupling reactions, offering a versatile tool for constructing complex molecular architectures.

Single-Electron-Transfer-Mediated Carbonylation Reactions

ConspectusTransition-metal-catalyzed carbonylation coupling methods have been accepted as an essential tool for producing carbonylated products over the past few decades. Despite its long-standing history and widespread industrial applications, several challenges remain in carbonylation chemistry. These include reliance on precious metal catalysts, the need of high-energy radiation, difficulties in carbonylation of unactivated chemical bonds, etc. As an alternative to classic two-electron transfer process, single-electron-transfer (SET)-mediated carbonylation has emerged as a powerful tool to achieve elusive carbonylation transformations. Over the past few years, carbonylation of commonly available functional handles, such as alkenes and alkyl halides, via the single-electron pathway has emerged as a valuable area of research.Our team has been dedicated to developing new carbonylation reactions using bulk chemicals to construct high-value carbonylated products. These reactions have broad synthetic and industrial applications, motivating us to explore SET-mediated carbonylation transformations for two key classes of bulk chemicals: alkanes and alkyl halides. Specifically, our work has centered on two main approaches: (1) Single-electron reduction of C(sp3)-X bonds: this strategy leverages single-electron reduction to activate C(sp3)-X bonds, promoting the formation of carbon radicals, which in turn promotes subsequent addition to metals or CO. However, a significant challenge lies in the highly negative reduction potential of certain substrates [Ered < -2 V compared to the saturated calomel electrode (SCE) for unactivated alkyl iodides]. Despite these challenges, the intrinsic reducibility of CO and the reactivity of various carbonyl-metal intermediates facilitate smooth reaction progress. (2) Single-electron oxidative of C(sp3)-H bonds: this strategy emphasizes efficiency, high atomic utilization, and minimal waste by bypassing traditional preactivation methods. Using 3d metal catalysts, we have successfully performed aminocarbonylation and alkoxycarbonylation on a wide range of C(sp3)-H bonds (such as those in aliphatic alkanes, ethers, amines, etc.). The above two approaches also enabled radical relay carbonylation of alkenes, allowing precise control over reaction intermediates and pathways. Such control improves both reaction efficiency and selectivity. These advancements have enabled transition metal or photoredox catalysis to facilitate radical relay carbonylation of unactivated alkenes, resulting in transformations such as oxyalkylative carbonylation, aminoalkylative carbonylation, fluoroalkylative carbonylation, double carbonylation, and rearrangement carbonylation.SET-mediated carbonylation significantly enhances the sustainability and scalability of the carbonylation process by reducing reliance on precious metal catalysts and enabling milder reaction conditions. Additionally, by carefully controlling reaction intermediates, we have fine-tuned the process to produce a wide range of carbonylation products with high selectivity. This flexibility expands the applications of carbonylation in synthetic chemistry and industrial processes. Finally, we place particular emphasis on the application of carbonylation reactions in drug discovery, where they serve as powerful functional handles for the late-stage modification of bioactive molecules. The broad applicability of SET-mediated carbonylation methods to various chemical bonds significantly enriches the toolbox for drug synthesis, enabling the efficient functionalization of complex molecules. This versatile approach has the potential to accelerate the discovery of novel therapeutic agents, making it a critical tool in modern medicinal chemistry.

An Electrochemical Design for a General Catalytic Carboxylic Acid Substitution Platform via Anhydrides at Room Temperature: Amidation, Esterification, and Thioesterification

An original concept for catalytic electrochemical dehydration has enabled a suite of acid substitutions, including amidation, esterification, and thioesterification, through a linchpin anhydride formed in situ. By avoiding stoichiometric dehydrating agents, this method addresses a leading challenge in organic synthesis and green chemistry. It also proceeds without acid additives at room temperature, accesses a diverse range of product structures, is easily scaled, and enabled the first example of catalytic peptide coupling at room temperature.

Merging Photoexcited Nitroarenes with Lewis Acid Catalysis for the Anti-Markovnikov Oxidation of Alkenes

Herein we describe the oxidation of alkenes to carbonyls and acetonides via the interplay of photoexcited nitroarenes and Lewis acid catalysis. A wide range of alkenes were oxidized to aldehyde and ketone products with anti-Markovnikov selectivity and to acetonides when acetone was employed as a co-solvent. Mechanistic studies support that Lewis acid coordination to the 1,3,2-dioxazolidine intermediate results in a 1,2-shift to generate carbonyl derivatives and a nucleophilic substitution pathway for the formation of acetonides.

Light-Dependent Amide or Thioamide Formation of Acylsilanes with Amines using Elemental Sulfur

Due to the diverse chemical and physical properties of functional groups, mild and controllable ligation methods are often required to construct complex drugs and functional materials. To make diverse sets of products with tunable physicochemical properties, it is also useful to employ complimentary ligation methods that adopt the same starting materials. Here, we disclose the efficient and modular synthesis of amides or thioamides through the chemical ligation of acylsilanes with amines, simply by turning a light on or off. This method is fast, mild, high-yielding and displays excellent functional-group tolerance. The versatility of these reactions is highlighted by their ability to perform post-synthetic modifications on a variety of marketed medications, peptides, natural substances, and compounds with biological activity. In-depth computational and experimental studies clarified the photo-dependent umpolung of reactivity of acylsilanes, namely: photoexcitation leads to nucleophilic O-silyl carbenes that react with S8 to form O-silyl thionoesters and eventually amides. In contrast, acylsilanes react as electrophiles with amines thermally in the dark, with C→O silyl transfer, prior to reacting with S8 to form thioamides. These mechanistic details are expected to guide the development of similar coupling reactions.

Exploring nickel-catalyzed organochalcogen synthesis via cross-coupling of benzonitrile and alkyl chalcogenols with computational tools

The preparation of organochalcogens has increased in recent times due to their promising biological activity properties. This work studies the reaction mechanism of a nickel(0)-catalyzed cross-coupling between benzonitrile and propanethiol to produce new C-S bonds by computational means. The proposed mechanism follows the classical oxidative addition/transmetalation/reductive elimination cross-coupling sequence, involving an unusual oxidative addition of a Ph-CN bond onto the active species. The computed catalytic cycle for thioether synthesis has been examined to determine whether the same protocol could be employed to build the analogous C-Se and C-Te bonds. The proposed mechanism for C-S coupling is validated by microkinetic modeling and shows a very good agreement with available experimental data. The extension of the proposed mechanism to C-Se and C-Te couplings indicates that these new reactions should be operative, although their reaction rates appear to be significantly slower.

EFGs: A Complete and Accurate Implementation of Ertl's Functional Group Detection Algorithm in RDKit

Functional groups are widely used in organic chemistry, because they provide a rationale to analyze physicochemical and reactivity properties. In medicinal chemistry, they are the basis for analyzing ligand-biomacromolecule interactions. Ertl's algorithm is an approach to extract functional groups in arbitrary organic molecules that does not depend on predefined libraries of functional groups. However, there is a lack of a complete and accurate implementation of Ertl's algorithm in the widely used RDKit cheminformatic toolkit. In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. For a RDKit molecule, it provides (i) a PNG binary string with an image of the molecule with color-highlighted functional groups; (ii) a list of sets of atom indices (idx), each set corresponding to a functional group; (iii) a list of pseudo-SMILES canonicalized strings for the full functional groups; and (iv) a list of RDKit labeled mol objects, one for each full functional group. The code is freely available in https://github.com/bbu-imdea/efgs and is part of the RDKit Contrib directory (https://github.com/rdkit/rdkit/tree/master/Contrib/efgs).

Radical trifluoromethoxylation of fluorinated alkenes for accessing difluoro(trifluoromethoxy)methyl groups

In this study, we explore the potential of the difluoro(trifluoromethoxy)methyl group, CF2-O-CF3, an underexplored but promising structural analog of the trifluoromethoxy group (OCF3). This moiety offers unique electronic properties and enhanced chemical stability due to its multiple C-F bonds, along with the added advantage of C-O bond cleavage, making it an attractive option in fluorine chemistry. We have succeeded in synthesizing difluoro(trifluoromethoxy)methyl compounds via radical amino- and hydroxy-trifluoromethoxylations of β,β-difluorostyrenes. Control experiments, including radical clock experiments, support a free radical mechanism. The synthetic utility of the resulting difluoro(trifluoromethoxy)methyl compounds is also demonstrated through transformations into bioactive analogs, such as pyrrole derivatives, fendiline analogs, and carpropamid analogs, highlighting their potential in drug development.

Oxenoid Reactivity Enabled by Targeted Photoactivation of Periodate

The chemistry of low-valent intermediates continues to inspire new modes of reactivity across synthetic chemistry. But while the generation and reactivity of both carbenes and nitrenes are well-established, difficulties in accessing oxene, their oxygen-based congener, has severely hampered its application in synthesis. Here, we report a conceptually novel approach towards oxenoid reactivity through the violet-light photolysis of tetrabutylammonium periodate. Computational studies reveal an unexpected geometric change upon periodate photoexcitation that facilitates intersystem crossing and near-barrierless dissociation of triplet periodate into oxene. Under these operationally simple conditions, we have demonstrated the epoxidation of a wide range of substituted olefins, revealing unprecedented functional group compatibility. By overcoming the historic challenges associated with employing oxene as an intermediate in organic chemistry, we believe that this platform will inspire the development of new reactive oxygen-based methodologies across industry and academia.

Selective Deuteration and Tritiation of Pharmaceutically Relevant Sulfoximines

Pharmaceutical-aligned research endeavors continue to diversify, including via the installation of new chemical functionality and non-classical bioisosteres within drug design. With this, an equally high demand emerges for the direct installation of isotopic substituents into these scaffolds within drug discovery programmes, as isotopologues are essential for the elucidation of the biological efficacy and metabolic fate of the active pharmaceutical ingredient (API). The sulfoximine functional group has recently become established as a high-value unit in this context; however, general and effective methods for the synthesis of deuterium (2H, D) and tritium (3H, T) labelled analogues have remained elusive. Herein, we disclose the design and development of the first iridium-catalyzed sulfoximine-directed hydrogen isotope exchange (HIE) systems that permit the site-selective integration of a distinguishing atomic label at aromatic C(sp2)-H and more challenging C(sp3)-H moieties. Moreover, we exemplify the broad applicability of these methods within a spectrum of molecular settings, as well as in the late-stage generation of isotopically-enriched complex bioactive architectures.

Deoxygenative photochemical alkylation of secondary amides enables a streamlined synthesis of substituted amines

Secondary amines are vital functional groups in pharmaceuticals, agrochemicals, and natural products, necessitating efficient synthetic methods. Traditional approaches, including N-monoalkylation and reductive amination, suffer from limitations such as poor chemoselectivity and complexity. Herein, we present a streamlined deoxygenative photochemical alkylation of secondary amides, enabling the efficient synthesis of α-branched secondary amines. Our method leverages triflic anhydride-mediated semi-reduction of amides to imines, followed by a photochemical radical alkylation step. This approach broadens the synthetic utility of amides, facilitating late-stage modifications of drug-like molecules and the synthesis of saturated N-substituted heterocycles. The pivotal role of flow technology in developing a scalable and robust process underscores the practicality of this method, significantly expanding the organic chemist's toolbox for complex amine synthesis.

How Do Microbial Metabolites Interact with Their Protein Targets?

The design of drugs and nutraceutics that mimic microbial metabolites is an emerging drug modality in medicinal chemistry that attempts to modulate the myriad of interactions that these molecules establish with host and microbial proteins. Understanding how microbial metabolites interact with their target proteins is key to perform a rational design of metabolite mimetic molecules for therapeutic usage. In the present work, we address this question by analyzing the functional groups of these molecules and the interactions they display in a set of more than 71K protein-metabolite interactions from the PDB. Significant differences in the functional group distributions, their chemical features, and their co-occurrences are observed for distinct subsets of these molecules. The same is true for the distributions of interaction types. By correlating both data sets, we are able to explain the observed interaction patterns in terms of observed functional group patterns. These results will shed light on the rational design of novel metabolite mimetic molecules for therapeutic purposes.

FON: An Innovative Fluorinated Group via Hydroetherification-Type Reactivity

An efficient strategy for preparing the novel O-difluoroalkylhydroxylamine fluorinated functional group, coined FON, is reported. This analogue of medicinally important β-phenethyl ether scaffolds in uniting gem-difluoro and N-O moieties is synthesized in one step via chemo- and regioselectivity metal-free hydroetherification-type additions. As shown, this unique mode of reactivity is realized for a diverse substrate scope and applied to gram-scale synthesis and site-selective deuterium incorporation. Lastly, a mechanistic understanding with implications in Brønsted acid catalysis is offered.

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.

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.

Defect-Engineered Metal-Organic Frameworks as Bioinspired Heterogeneous Catalysts for Amide Bond Formation

The synthesis of amides from amines and carboxylic acids is the most widely carried out reaction in medicinal chemistry. Yet, most amide couplings are still conducted using stoichiometric reagents, leading to significant waste; few synthetic catalysts for this transformation have been adopted industrially due to their limited scope and/or poor recyclability. The majority of catalytic approaches focus on a single activation mode, such as enhancing the electrophilicity of the carboxylic acid partner using a Lewis acid. In contrast, nature effortlessly forges and breaks amide bonds using precise arrays of Lewis/Brønsted acidic and basic functional groups. Drawing inspiration from these systems, herein we report a simple defect engineering strategy to colocalize Lewis acidic Zr sites with other catalytically active species within porous metal-organic frameworks (MOFs). Specifically, the combination of pyridine N-oxide and Zr open metal sites within the defective framework MOF-808-py-Nox produces a heterogeneous catalyst that facilitates amide bond formation with broad functional group compatibility from amines and carboxylic acids, esters, or primary amides. Extensive density functional theory (DFT) calculations using cluster models support that the formation of a hydrogen-bonding network at the defect sites facilitates amide bond formation in this material. MOF-808-py-Nox can be recycled at least five times without losing significant crystallinity, porosity, or catalytic activity and can be employed in continuous flow. This defect engineering strategy can be potentially generalized to produce libraries of catalytically active MOFs with different combinations of colocalized functional groups.

Organophotocatalytic Reduction of Benzenes to Cyclohexenes

The reduction of abundant benzene rings to scarce C(sp3)-rich motifs is invaluable for drug design, as C(sp3) content is known to correlate with clinical success. Cyclohexenes are attractive targets, as they can be rapidly elaborated into large product libraries and are stable against rearomatization. However, partial reduction reactions of benzenes to cyclohexenes are rare and have a very narrow scope. Herein we report a broadly applicable method that converts electron-poor benzenes to cyclohexenes and tolerates Lewis-basic functional groups such as triazoles and thioethers as well as reducible groups such as cyanides, alkynes, and sulfones. The reaction utilizes an organic donor that induces mild arene reduction by preassociation to a photoexcitable electron donor-acceptor (EDA) complex and mild isomerization of redox-inert 1,4-cyclohexadienes to reducible 1,3-cyclohexadienes without a strong base in its oxidized thioquinone methide form.

Iterative One-Carbon Homologation of Unmodified Carboxylic Acids

The one-carbon homologation of carboxylic acids is a valuable route to construct families of homologues, which play fundamental roles in chemistry and biology. However, known procedures are based on multistep sequences, use harsh conditions or are limited in scope. Thus, almost a century after the discovery of the original Arndt-Eistert homologation sequence, a general method to directly convert carboxylic acids into their corresponding homologues remains elusive. Exploiting the photoredox reactivity of nitroethylene, we disclose a practical visible-light-induced homologation of unmodified carboxylic acids. Iterations of the procedure reveal an exceptionally tunable strategy for the construction of inert carbon spacers, opening new opportunities in synthesis.

Nickel Catalyzed Carbonylative Cross Coupling for Direct Access to Isotopically Labeled Alkyl Aryl Ketones

Here we present an effective nickel-catalyzed carbonylative cross-coupling for direct access to alkyl aryl ketones from readily accessible redox-activated tetrachlorophthalimide esters and aryl boronic acids. The methodology, which is run employing only 2.5 equivalents of CO and simple Ni(II) salts as the metal source, exhibits a broad substrate scope under mild conditions. Furthermore, this carbonylation chemistry provides an easy switch between isotopologues for stable (13CO) and radioactive (14CO) isotope labeling, allowing its adaptation to the late-stage isotope labeling of pharmaceutically relevant compounds. Based on DFT calculations as well as experimental evidence, a catalytic cycle is proposed involving a carbon-centered radical formed via nickel(I)-induced outer-sphere decarboxylative fragmentation of the redox-active ester.

Structure Elucidation of Pharmaceutically Relevant Compounds Within Pyrene-Based Frameworks

Single-crystal X-ray diffraction (SCXRD) is the preferred and most accurate technique for determining molecular structures. However, it can present challenges when dealing with specific small molecules and active pharmaceutical ingredients (APIs), as many do not form quality crystals without coformers or can be unstable. In this study, we introduce tetrakis(guanidinium) pyrenetetrasulfonate (G4PYR), a robust guanidinium-organosulfonate (GS) framework that efficiently encapsulates small molecules and APIs rich in functional groups. The hydrogen bonding frameworks formed by G4PYR display well-ordered structures with predictable pyrene-pyrene distances, making them ideally suited for targeting arene-based APIs with pendant groups. Successful encapsulation of various guests, including benzaldehyde, benzamide, and arenes containing multiple hydrogen bond donors and acceptors like uracil and thymine, was achieved. Furthermore, we successfully encapsulated important pharmaceutical and biologically relevant compounds, such as lidocaine, ropinirole, adenosine, thymidine, and others. Notably, we present a workflow for investigating host-guest complex formation using powder X-ray diffraction and high throughput experimentation.

Ligand-controlled palladium-catalyzed regiodivergent aminocarbonylation of tert-alcohols

Alcohols are widely available, abundant, and diverse in both commercial and natural resources. They possess low toxicity, making their use as reactants for carbonylation extremely promising. Herein, we present a robust ligand-controlled regioselective aminocarbonylation of tert-alcohols. Utilizing a commercially available palladium salt and ligand as the catalytic system, various amides containing an α-quaternary carbon or β-substituted amides can be selectively accessible. Notably, water is the only by-product of this reaction, which is consistent with the concept of green chemistry. This protocol offers a broad substrate scope, high regioselectivity, and excellent performance in scale-up reactions.

The freedom space - a new set of commercially available molecules for hit discovery

The advent of high-performance virtual screening techniques nowadays allows drug designers to explore ultra-large sets of candidate compounds in search of molecules predicted to have desired properties. However, the success of such an endeavor heavily relies on the pertinence (drug-likeness and, foremost, chemical feasibility) of these candidates, or otherwise, virtual screening will return valueless "hits", by the garbage in/garbage out principle. The huge popularity of the judiciously enumerated Enamine REAL Space is clear proof of the strength of this Big Data trend in drug discovery. Here we describe a new dataset of make-on-demand compounds called the Freedom space. It follows the principles of Enamine REAL Space and contains highly feasible molecules (synthesis success rate over 75 percent). However, the scaffold and chemography analysis revealed significant differences to both the REAL and biologically annotated compounds from the ChEMBL database. The Freedom Space is a significant extension of the REAL Space and can be utilized for a more comprehensive exploration of the synthetically feasible chemical space in hit finding and hit-to-lead campaigns.

A Ni(II)MOF-based hypersensitive dual-function luminescent sensor towards the 3-nitrotyrosine biomarker and 6-propyl-2-thiouracil antithyroid drug in urine

Trace detection of bioactive small molecules (BSMs) in body fluids is of great importance for disease diagnosis, drug discovery, and health monitoring. Based on the chiral ligand of 4,4'-(1,2-dihydroxyethane-1,2-diyl)dibenzoic acid (H2L), an achiral 3D porous Ni(II)-MOF, with a trinuclear cluster based (3,9)-c {42·6}3{46·621·89}-xmz net, was constructed under solvothermal conditions. Benefiting from its robust framework and excellent luminescent performance, NiMOF was endowed with remarkable capabilities in efficiently, rapidly, and sensitively detecting the 3-nitrotyrosine (3-NT) biomarker and 6-propyl-2-thiouracil (6-PTU) thyroid drug based on the spectral overlap and photo-induced electron transfer (PET) caused luminescence quenching response. Notably, NiMOF exhibited exceptional performance in quantifying 3-NT and 6-PTU in urine samples, yielding highly satisfactory results. Additionally, an intelligent detection system was crafted to enhance the reliability and practicability of 3-NT/6-PTU detection in urine, based on tandem combinational logic gates. This work not only heralds a promising trajectory in the development of MOF-based luminescent sensors, but also paves the way for the intelligent monitoring of BSMs in real bodily fluids.

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.

Rapid and General Amination of Aryl Boronic Acids and Esters Using O-(Diphenylphosphinyl)hydroxylamine (DPPH)

O-(Diphenylphosphinyl)hydroxylamine (DPPH) is a general reagent for the conversion of (hetero)aryl boronic acids and esters to primary anilines. The transformation proceeds rapidly at rt and exhibits a broad substrate scope and exceptional functional-group tolerance. In terms of rate, the reaction is relatively insensitive to the electronic properties of the substrate, in contrast to similar reactions using electrophilic amination reagents such as hydroxylamine-O-sulfonic acid. Consequently, this protocol is particularly useful for accessing electron-deficient (hetero)aryl anilines, which had been challenging to prepare using prior methods.

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 Asymmetric Synthesis of α-Aminoimines from 1,2-Bis-N-Sulfinylimines by Using Allyl Boronic Acids

A unique direct asymmetric synthesis of α-aminoimines is realized, through rapid and exclusive mono-allylation of chiral bis-N-sulfinylimines using allylboronic acids. The highly selective allylation was possible as electrophilic imine functional group in the product α-aminoimines remained unreactive towards allyl boronic acid nucleophiles. Notably, by varying the geometry and chiral auxiliary, all four isomers of the α-aminoimines were accessed from readily available precursors. A range of allyl nucleophiles, which are tricky to generate by other means possessing highly reactive functional groups also took part in this reaction, expanding the scope further. The applicability of the products α-aminoimines were further demonstrated by accessing a range of structurally diverse chiral cyclic and acyclic 1,2-diamines bearing adjacent stereocenters through addition of a second nucleophile or Prins-type cyclization by exploiting the nucleophilicity of the tethered alkene moiety. Moreover, the leaving group aptitude of sulfinyl auxiliary attached to imine, was exploited to access valuable chiral α-aminonitriles under thermal conditions without employing any reagents. Detailed DFT calculation revealed a chair-like transition state, arising from corresponding allylboroxine species, likely operating for the allylboration reaction across imine.

The IMS Library: from IN-Stock to Virtual

A chemical library is a key element in the early stages of pharmaceutical research. Its design encompasses various factors, such as diversity, size, ease of synthesis, aimed at increasing the likelihood of success in drug discovery. This article explores the collaborative efforts of computational and synthetic chemists in tailoring chemical libraries for cost-effective and resource-efficient use, particularly in the context of academic research projects. It proposes chemoinformatics methodologies that address two pivotal questions: first, crafting a diverse panel of under 1000 compounds from an existing pool through synthetic efforts, leveraging the expertise of organic chemists; and second, expanding pharmacophoric diversity within this panel by creating a highly accessible virtual chemical library. Chemoinformatics tools were developed to analyse initial panel of about 10,000 compounds into two tailored libraries: eIMS and vIMS. The eIMS Library comprises 578 diverse in-stock compounds ready for screening. Its virtual counterpart, vIMS, features novel compounds guided by chemists, ensuring synthetic accessibility. vIMS offers a broader array of binding motifs and improved drug-like characteristics achieved through the addition of diverse functional groups to eIMS scaffolds followed by filtering of reactive or unusual structures. The uniqueness of vIMS is emphasized through a comparison with commercial suppliers' virtual chemical space.

Electrochemical Non-Directed Arene C-H Amination

Electrosynthesis represents a dynamic field in organic chemistry for the development of important and selective reactions. Among the most interesting electrosynthetic transformations is the non-directed arene C-H amination. Despite increasing reports, the quest for a non-directed electrochemical arene C-H amination capable of accommodating a wide range of arenes and amines with high site-selectivity remains ongoing. Non-directed electrochemical C-H amination presents a metal-free, mild approach for synthesizing complex aminated compounds of interest in pharmaceuticals and natural products. This concept aims to introduce the concept of non-directed electrochemical C-H amination and provide an overview of the recent advances in the field as well as the current limitations and potential directions.

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.

Palladium-catalyzed cross-coupling of alcohols with olefins by positional tuning of a counteranion

Transition metal-catalyzed cross-couplings have great potential to furnish complex ethers; however, challenges in the C(sp3)-O functionalization step have precluded general methods. Here, we describe computationally guided transition metal-ligand design that positions a hydrogen-bond acceptor anion at the reactive site to promote functionalization. A general cross-coupling of primary, secondary, and tertiary aliphatic alcohols with terminal olefins to furnish >130 ethers is achieved. The mild conditions tolerate functionality that is prone to substitution, elimination, and epimerization and achieve site selectivity in polyol settings. Mechanistic studies support the hypothesis that the ligand's geometry and electronics direct positioning of the phosphate anion at the π-allyl-palladium terminus, facilitating the phosphate's hydrogen-bond acceptor role toward the alcohol. Ligand-directed counteranion positioning in cationic transition metal catalysis has the potential to be a general strategy for promoting challenging bimolecular reactivity.

Enantioselective synthesis of γ-chiral amides via copper-catalyzed reductive relay hydroaminocarbonylation

Chiral amides are common and effective structural motifs found in many pharmaceuticals and biologically active molecules. Despite their importance, existing synthetic methods are predominantly employed for the synthesis of α-amides and β-amides. The synthesis of remote chiral amides, characterized by distal stereocenters, typically requires intricate synthetic steps conducted under demanding conditions. Here, we present a general procedure for the copper-catalyzed enantioselective synthesis of γ-chiral amides, employing a reductive relay hydroaminocarbonylation strategy with trisubstituted allylic benzoates and hydroxylamine electrophiles. This approach demonstrates a wide substrate scope with excellent enantioselectivity and regioselectivity, thus providing access to challenging enantioenriched γ-chiral amides.

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.

1-Iodoglycal: A Versatile Intermediate for the Synthesis of d-Glyco Amides and Esters Employing Carbonylative Cross-Coupling Reaction

In this study, we present the development of two catalytic processes: a Pd-PEPPSI-catalyzed aminocarbonylation and a Pd(OAc)2-Xantphos-catalyzed alkoxycarbonylation of d-glycals, utilizing carbonylative cross-coupling reactions. We explored successfully various types of aromatic amines, as well as alkyl amines and amino acids, to synthesize new d-glycal amides. However, we observed limitations in the reactivity of alkyl and heteroaromatic amines. The processes enabled the synthesis of 20 novel C1-branched glycoamides and 7 new d-gluco esters.

Fcg-Former: Identification of Functional Groups in FTIR Spectra Using Enhanced Transformer-Based Model

Deep learning (DL) is becoming more popular as a useful tool in various scientific domains, especially in chemistry applications. In the infrared spectroscopy field, where identifying functional groups in unknown compounds poses a significant challenge, there is a growing need for innovative approaches to streamline and enhance analysis processes. This study introduces a transformative approach leveraging a DL methodology based on transformer attention models. With a data set containing approximately 8677 spectra, our model utilizes self-attention mechanisms to capture complex spectral features and precisely predict 17 functional groups, outperforming conventional architectures in both functional group prediction accuracy and compound-level precision. The success of our approach underscores the potential of transformer-based methodologies in enhancing spectral analysis techniques.

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.

A Hierarchical Graph Neural Network Framework for Predicting Protein-Protein Interaction Modulators With Functional Group Information and Hypergraph Structure

Accurate prediction of small molecule modulators targeting protein-protein interactions (PPIMs) remains a significant challenge in drug discovery. Existing machine learning-based models rely on manual feature engineering, which is tedious and task-specific. Recently, deep learning models based on graph neural networks have made remarkable progress in molecular representation learning. However, many graph-based approaches ignore molecular hierarchical structure modeling guided by domain knowledge. In chemistry, the functional groups of a molecule determine its interaction with specific targets. Therefore, we propose a hierarchical graph neural network framework (called HiGPPIM) for predicting PPIMs by integrating atom-level and functional group-level features of molecules. HiGPPIM constructs atom-level and functional group-level graphs based on chemical knowledge and learns graph representations using graph attention networks. Furthermore, a hypergraph attention network is designed in HiGPPIM to aggregate and transform two-level graph information. We evaluate the performance of HiGPPIM on eight PPI families and two prediction tasks, namely PPIM identification and potency prediction. Experimental results demonstrate that HiGPPIM achieves state-of-the-art performance on both tasks and that using functional group information to guide PPIM prediction is effective.

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.

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).