De novo branching cascades for structural and functional diversity in small molecules

n-Tuples on Scaffold Diversity Inspired by Drug Hybridisation to Enhance Drugability: Application to Cytarabine

A mathematical concept, n-tuples are originally applied to medicinal chemistry, especially with the creation of scaffold diversity inspired by the hybridisation of different commercial drugs with cytarabine, a synthetic arabinonucleoside derived from two marine natural products, spongouridine and spongothymidine. The new methodology explores the virtual chemical-factorial combination of different commercial drugs (immunosuppressant, antibiotic, antiemetic, anti-inflammatory, and anticancer) with the anticancer drug cytarabine. Real chemical combinations were designed and synthesised for 8-duples, obtaining a small representative library of interesting organic molecules to be biologically tested as proof of concept. The synthesised library contains classical molecular properties regarding the Lipinski rules and/or beyond rules of five (bRo5) and is represented by the covalent combination of the anticancer drug cytarabine with ibuprofen, flurbiprofen, folic acid, sulfasalazine, ciprofloxacin, bortezomib, and methotrexate. The insertion of specific nomenclature could be implemented into artificial intelligence algorithms in order to enhance the efficiency of drug-hunting programs. The novel methodology has proven useful for the straightforward synthesis of most of the theoretically proposed duples and, in principle, could be extended to any other central drug.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Synthesis and medicinal chemistry of tetronamides: Promising agrochemicals and antitumoral compounds

Butenolides and tetronic acids occupy a prominent position in synthetic chemistry due to their ubiquitous distribution in nature. This has stimulated investigations firstly in the synthesis of such systems and, laterly, the interest has turned to the understanding of the quantum structure of such systems, allowing a deeper understanding of the mechanism and reactivity of this cyclic scaffold. In contrast, tetronamides, which consist of compounds bearing a 4-aminofuran-2(5H)-one backbone, are relatively rare in nature and synthetic routes to such compounds are poorly explored. This review highlights both the importance of the tetronamide scaffold in medicinal chemistry and the most relevant recondite synthetic strategies for obtaining compounds of this class.

Catalytic asymmetric transformation of nitrones and allenes to dihydropyridoindoles via chiral N,N'-dioxide/cobalt(II) catalysis

A chiral N,N'-dioxide/cobalt(II) complex catalytic system is developed to promote the multistep cascade reaction of α,β-unsaturated-N-aryl nitrones with allenes, giving a variety of chiral dihydropyridoindoles in moderate to good yields with excellent dr and ee values. Mechanistic studies support a [3+2] cycloaddition/[3,3]-rearrangement/retro-Mannich process.

Direct Prediction of Bioaccumulation of Organic Contaminants in Plant Roots from Soils with Machine Learning Models Based on Molecular Structures

Root concentration factor (RCF) is an important characterization parameter to describe accumulation of organic contaminants in plants from soils in life cycle impact assessment (LCIA) and phytoremediation potential assessment. However, building robust predictive models remains challenging due to the complex interactions among chemical-soil-plant root systems. Here we developed end-to-end machine learning models to devolve the complex molecular structure relationship with RCF by training on a unified RCF data set with 341 data points covering 72 chemicals. We demonstrate the efficacy of the proposed gradient boosting regression tree (GBRT) model based on the extended connectivity fingerprints (ECFP) by predicting RCF values and achieved prediction performance with R-squared of 0.77 and mean absolute error (MAE) of 0.22 using 5-fold cross validation. In addition, our results reveal nonlinear relationships among properties of chemical, soil, and plant. Further in-depth analyses identify the key chemical topological substructures (e.g., -O, -Cl, aromatic rings and large conjugated π systems) related to RCF. Stemming from its simplicity and universality, the GBRT-ECFP model provides a valuable tool for LCIA and other environmental assessments to better characterize chemical risks to human health and ecosystems.

Nickel(II)-Catalyzed [3 + 2] Cycloaddition of Nitrones and Allenoates to Access N-Vinylindoles and N-Vinylpyrroles

A variety of N-vinylindoles and N-vinylpyrroles were prepared in moderate to good yields through the nickel(II)-catalyzed [3 + 2] cycloaddition of α,β-unsaturated nitrones with allenoates under mild reaction conditions. A rational mechanism for the formation of N-vinylindoles was proposed based on the ¹⁸O-labeled experiments and key intermediates detected by high-resolution mass spectrometry trace experiments. The present method highlights a nickel(II)-controlled cyclization, atom-economical reaction, broad substrate scope, good functional group tolerance, and high Z-stereoselectivity for the enamine bond.

Hypothetical control of postural sway

Quiet standing exhibits strongly intermittent variability that has inspired at least two interpretations. First, variability can be intermittent through the alternating engagement and disengagement of complementary control processes at distinct scales. A second and perhaps deeper way to interpret this intermittency is through the possibility that postural control depends on cascade-like interactions across many timescales at once, suggesting specific non-Gaussian distributional properties at different timescales. Multiscale probability density function (PDF) analysis shows that quiet standing on a stable surface exhibits a crossover from low, increasing non-Gaussianity (consistent with exponential distributions) at shorter timescales, reflecting inertial control, towards higher non-Gaussianity. Feedback-based control at medium to longer timescales yields a linear decrease that is characteristic of cascade dynamics. Destabilizing quiet standing with an unstable surface or closed eyes serves to attenuate inertial control and to elicit more of the feedback-based control over progressively shorter timescales. The result was to strengthen the appearance of the linear decay indicating cascade dynamics. Finally, both linear and nonlinear indices of postural sway also govern the relative strength of crossover or of linear decay, suggesting that tempering of non-Gaussianity across log-timescale is a function of both extrinsic constraints and endogenous postural control. These results provide new evidence that cascading interactions across longer timescales supporting postural corrections can even recruit shorter timescale processes with novel task constraints that can destabilize posture.

Gold(iii)-catalyzed bicyclizations of alkylidenecyclopropane-tethered ynones for divergent synthesis of indene and naphthalenone-based polycycles

A gold(iii)-catalyzed cascade oxidation/cyclization of alkylidenecyclopropane-tethered ynones for the assembly of indene and naphthalenone-based polycycles by employing different N-oxides is reported.

Two Completely Orthogonal Quorum Sensing Systems with Self-Produced Autoinducers Enable Automatic Delayed Cascade Control

The existence of crosstalk between quorum sensing systems limits their application in a complex environment. In this study, two completely orthogonal quorum sensing systems with self-produced autoinducers were built in one cell to enable the systems to be signal orthogonal and promoter orthogonal to each other. The systems were designed on the basis of the las system from Pseudomonas aeruginosa and the tra system from Agrobacterium tumefaciens. Both were optimized with respect to the orthogonality of signals and promoters by using a series of synthetic biology strategies and high-throughput screening. The systems were applied intracellularly, and an automatic delayed cascade circuit was successfully demonstrated, which can realize sequential gene expression without exogenous inducer. This circuit provides a new tool for biotechnological applications, such as metabolic regulation, that require sequential gene control. This cascade model expands the toolkit of synthetic biology research and indicates a high application potential of quorum sensing systems that are orthogonal to each other.

Remarkable Potential of Zerumbone to Generate a Library with Six Natural Product-like Skeletons by Natural Material-Related Diversity-Oriented Synthesis

Diversity-oriented synthesis (DOS) is an effective strategy for the quick creation of diverse and high three-dimensional compounds from simple starting materials. The selection of a starting material is the key to constructing useful, chemically diverse compound libraries for the development of new drugs. Here, we report a novel, general, and facile strategy for the creation of diverse compounds with high structural diversity from readily available natural products, such as zerumbone, as the synthetic starting material. Zerumbone is the major component of the essential oil from wild ginger, Zingiber zerumbet Smith. It is noteworthy that zerumbone has a powerful latent reactivity, partly because of its three double bonds, two conjugated and one isolated, and a double conjugated carbonyl group in an 11-membered ring structure. In fact, zerumbone has been shown to be a successful example of natural material-related DOS (NMRDOS). We will report that zerumbone can be converted in one chemical step from four zerumbone derivatives into rare and markedly different scaffolds by transannulation.

RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions

Motivation

Molecular scaffolds are useful in medicinal chemistry to describe, discuss and visualize series of chemical compounds, biochemical transformations and associated biological properties.

Results

Here, we present RxnBLAST as a web-based tool for analyzing scaffold transformations and reactive chemical environment features in bioreactions. RxnBLAST extracts chemical features from bioreactions including atom–atom mapping, reaction centers, rules and functional groups to help understand chemical compositions and reaction patterns. Core-to-Core is proposed, which can be utilized in scaffold networks and for constructing a reaction space, as well as providing guidance for subsequent biosynthesis efforts.

Availability and implementation

RxnBLAST is available at: http://design.rxnfinder.org/rxnblast/.

Aza-Henry and aza-Knoevenagel reactions of nitriles for the synthesis of pyrido[1,2-a]indoles

N-(Propargyl)indole-2-carbonitriles undergo DBU-catalyzed addition of CH-acids to nitriles, followed by cyclization to give 9-aminopyrido[1,2-a]indoles.

Catalyst-controlled formal [4 + 1] annulation of N-vinyl fluorenone nitrones and allenoates to prepare spirofluorenylpyrrolines

A simple gimeracil-controlled formal [4 + 1] annulation was developed to prepare various spirofluorenylpyrrolines in good yields with high diastereoselectivity from N-vinyl fluorenone nitrones and allenoates.

Carbonyl-Directed Addition of N-Alkylhydroxylamines to Unactivated Alkynes: Regio- and Stereoselective Synthesis of Ketonitrones

A variety of ketonitrones were synthesized in moderate to excellent yields with high chemo-, regio-, and stereoselectivity by using carbonyl-directed addition of N-alkylhydroxylamines to unactivated alkynes under mild conditions. The product diverisity could be controlled by the use of different bases, and EtN( n-Pr)₂ could promote the formation of ketonitrones while using EtONa as base led to indanone-derived nitrones. Control experiments indicated that the carbonyl group of the substrate acted as an H-bond acceptor except for an electron-withdrawing group, and conjugated enone skeleton accounted for the high selectivity.

Synthesis of Cyclopropanoids via Substrate-Based Cyclization Pathways

A series of unexpected reactions triggered by the dimethyloxosulfonium methylide led to the discovery of unconventional approaches for the synthesis of cyclopropa-fused tetralones and indeno-spirocyclopropanes. These highly functionalized structures were further elaborated in one step to privileged scaffolds such as tetralones, indenones, and fluorenones. As a whole, the results presented herein establish new diversity-oriented folding pathways.

Cascade reaction based synthetic strategies targeting biologically intriguing indole polycycles

In this review, cascade reaction based synthesis strategies delivering biologically intriguing indole polycycles are presented.

Catalyst-controlled cascade synthesis of bridged bicyclic tetrahydrobenz[b]azepine-4-ones

A new cascade reaction provides convergent access to novel bridged bicyclic medium-sized N-heterocycles.

Mechanism-Guided Scaffold Diversification: Perturbing and Trapping the Intermediates of Maltol-Type Cascade Claisen Rearrangement

A mechanism-guided study to harness different kinds of active species in the cascade Claisen rearrangement for scaffold diversification has been developed. These robust and practical processes furnished a series of architectures with a large chemical space, varying from planar to three-dimensional. In addition, several interesting reactions were observed, such as [3 + 3] dimerization, quinone-based vinylogous Nazarov-type cyclization, and a rare 12e [σ2a + π2s + π2a + π2s + (π2a + π2s)] Mobius aromatic transition state mediated rearrangement.

Samarium(II) folding cascades involving hydrogen atom transfer for the synthesis of complex polycycles

The expedient assembly of complex, natural product-like small molecules can deliver new chemical entities with the potential to interact with biological systems and inspire the development of new drugs and probes for biology. Diversity-oriented synthesis is a particularly attractive strategy for the delivery of complex molecules in which the 3-dimensional architecture varies across the collection. Here we describe a folding cascade approach to complex polycyclic systems bearing multiple stereocentres mediated by reductive single electron transfer (SET) from SmI₂. Simple, linear substrates undergo three different folding pathways triggered by reductive SET. Two of the radical cascade pathways involve the activation and functionalization of otherwise inert secondary alkyl and benzylic groups by 1,5-hydrogen atom transfer (HAT). Combination of SmI₂, a privileged reagent for cascade reactions, and 1,5-HAT can lead to complexity-generating radical sequences that unlock access to diverse structures not readily accessible by other means.

A divergent synthetic pathway for pyrimidine-embedded medium-sized azacycles through an N-quaternizing strategy

A new divergent synthetic pathway for skeletally distinct pyrimidine-containing medium-sized azacycles was developed. Diversity-generating reactions via selective bond cleavages or migrations from N-quaternized intermediates were designed, and 14 discrete core skeletons were synthesized in an efficient manner. The skeletal diversity of the resulting molecular frameworks was confirmed by chemoinformatic analysis.

Medium-sized heterocycles have recently received significant attention because of their potential roles as modulators of protein–protein interactions, but their molecular diversity and synthetic availability are still inadequate to meet the demand. To address these issues, we developed a new divergent synthetic pathway for skeletally distinct pyrimidine-containing medium-sized azacycles. We introduced N-quaternized pyrimidine-containing polyheterocycles as novel key intermediates for diversity-generating reactions via selective bond cleavages or migrations and prepared 14 discrete core skeletons in an efficient manner. The skeletal diversity of the resulting molecular frameworks was confirmed by chemoinformatic analysis.

A biosynthesis-inspired approach to over twenty diverse natural product-like scaffolds

A synthetic approach to diverse scaffolds was developed that was inspired by diterpene biosynthesis. Initial scaffolds, generated using Diels-Alder reactions of furyl-functionalised amines, were transformed into alternative scaffolds using cleavage, ring expansion, annulation and rearrangement reactions. In total, 25 diverse scaffolds were prepared that were shown to have high natural product-likeness.

The dual reactivity of Weinreb amides applied to the late-stage divergent functionalisation of meso pyrrolidines

The dual reactivity of Weinreb amides was exploited to prepare diversified symmetrical and dissymmetrical 2,5-disubstituted pyrrolidines from simple building blocks.

Structure-Based Kinetic Control in a Domino Process: A Powerful Tool Toward Molecular Diversity in Chromone Series

Two successive original routes leading to two novel families of polyheterocycles starting from the versatile chromone-based Michael acceptors platform are reported herein. The major aspect of this work is the selective access to these frameworks by changing the course of the domino process involved in their formation. First, enaminochromanones were selectively accessed under uncommon kinetic control. In this study, we showed that the tuning of the selectivity toward the kinetic product could be achieved by key structural modifications of the different reaction partners involved in the domino process. Once selectivity was efficiently controlled, enaminochromanones were ultimately transformed into a more complex family of polyheterocycles containing the pyrrolo-oxazinone framework. Here, the modulation of the domino sequence toward these particularly scarce structures was enabled by a pivotal switch in reactivity induced by aryl-λ³-iodanes.

Catalytic Divergent [3+3]- and [3+2]-Cycloaddition by Discrimination Between Diazo Compounds

Highly selective divergent cycloaddition reactions of enoldiazo compounds and α-diazocarboximides catalyzed by copper(I) or dirhodium(II) have been developed. With tetrakis(acetonitrile)copper(I) tetrafluoroborate as the catalyst epoxypyrrolo[1,2-a]azepine derivatives were prepared in good yields and excellent diastereoselectivities through the first reported [3+3]-cycloaddition of a carbonyl ylide. Use of Rh2 (pfb)4 or Rh2 (esp)2 directs the reactants to regioselective [3+2]-cycloaddition generating cyclopenta[2,3]pyrrolo[2,1-b]oxazoles with good yields and excellent diastereoselectivities.

A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

Synthetic methods that efficiently construct structurally diverse molecular scaffolds are attractive routes to diversely bioactive molecules. Here the authors report a method whereby common starting materials are converted to structurally and functionally diverse products by changing the catalyst ligand.

Evaluating New Chemistry to Drive Molecular Discovery: Fit for Purpose?

As our understanding of the impact of specific molecular properties on applications in discovery-based disciplines improves, the extent to which published synthetic methods meet (or do not meet) desirable criteria is ever clearer. Herein, we show how the application of simple (and in many cases freely available) computational tools can be used to develop a semiquantitative understanding of the potential of new methods to support molecular discovery. This analysis can, among other things, inform the design of improved substrate scoping studies; direct the prioritization of specific exemplar structures for synthesis; and substantiate claims of potential future applications for new methods.

Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction

Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.

Synthesis of Natural Product-like Polyheterocycles via One-Pot Cascade Oximation, C-H Activation, and Alkyne Annulation

An efficient protocol for the direct transformation of chroman-4-ones to tricyclic fused pyridines with the skeleton of cassiarins, a family of alkaloids with antimalarial activity, was developed. Also, a general strategy for modular construction of polyheterocycles with diverse natural product-like skeletons was developed by using ketone-alkyne bifunctional substrates. These reactions involved a one-pot cascade oximation of ketones, rhodium-catalyzed C-H activation, and intermolecular/intramolecular alkyne annulations under mild conditions with high atom, step, and redox economy.

Stereoselective Domino Carbocyclizations of γ- and δ-Cyano-N-tosylhydrazones with Alkenylboronic Acids with Formation of Two Different C(sp(3))-C(sp(2)) Bonds on a Quaternary Stereocenter

A novel strategy for the synthesis of functionalized carbocycles is defined, through the cascade carbocyclization of alkenylboronic acids with δ- or γ-cyano-N-tosylhydrazones. In the reaction, two C(sp(3))-C(sp(2)) bonds are formed on the former hydrazonic carbon generating an all-carbon quaternary stereocenter, and leading to cyclic ketones featuring an alkenyl side chain with complete diastereoselectivity. The processes are conducted under very simple experimental conditions, only in the presence of K2CO3, in 1,4-dioxane as solvent and under microwave irradiation, and have been applied for the synthesis of a wide structural variety of fused cyclopentanones and cyclohexanones. Moreover, the versatility of this methodology has been demonstrated in the structural modification of androsterone.

Synthetic Small Molecule Inhibitors of Hh Signaling As Anti-Cancer Chemotherapeutics

The hedgehog (Hh) pathway is a developmental signaling pathway that is essential to the proper embryonic development of many vertebrate systems. Dysregulation of Hh signaling has been implicated as a causative factor in the development and progression of several forms of human cancer. As such, the development of small molecule inhibitors of Hh signaling as potential anti-cancer chemotherapeutics has been a major area of research interest in both academics and industry over the past ten years. Through these efforts, synthetic small molecules that target multiple components of the Hh pathway have been identified and advanced to preclinical or clinical development. The goal of this review is to provide an update on the current status of several synthetic small molecule Hh pathway inhibitors and explore the potential of several recently disclosed inhibitory scaffolds.

Oxadendralenes in asymmetric organocatalysis for the construction of tetrahydroisochromenes

Oxadendralenes are integrated in a novel manner into a one-pot cascade utilizing synergistic catalysis for the construction of valuable and complex bicyclic heterocyclic scaffolds. The construction is based on the organocatalytic activation of the oxadendralenes generating a vinylogous iminium-ion intermediate which is set-up for a 1,6-addition with an enamine formed from an aldehyde and the same organocatalyst. This reaction generates a cyclic oxadendralenic intermediate, which acts as an electron-deficient heterodiene reacting in a Lewis-acid catalyzed hetero-Diels-Alder reaction with vinyl ethers to form tetrahydroisochromenes with five continuous stereocenters in high yields, >20 : 1 dr and 99% ee. This synergistic organo- and Lewis-acid catalysed system also displays high tolerance for variation in oxadendralenes and aldehydes, which provides tetrahydroisochromenes with high diversity in the substituent pattern and the same excellent stereoselectivities. Mechanistic studies have been performed to account for the activation modes and stereochemical outcome of the reaction. The reaction concept has been extended to also include a sequential organocatalytic reaction of oxadendralenes with aldehydes, in which the enamine formed from the aldehyde and the organocatalyst act both in the first catalytic cycle forming the cyclic oxadendralenic intermediate and in a second catalytic cycle leading to tetrahydroisochromenes in good yields and excellent stereoselectivities. Mechanistic studies reveal that the stereochemistry of the organocatalyst has an influence on the diastereoselectivity of the reaction sequence. Some transformations of the tetrahydroisochromenes are also presented. The chiral tetrahydroisochromenes formed might be applied in the diversified synthesis of important drugs.