Copper(I)‐Catalyzed Interrupted Click Reaction: Synthesis of Diverse 5‐Hetero‐Functionalized Triazoles

The 5‐heterofunctionalized triazoles are important scaffolds in bioactive compounds, but current click reactions (CuAAC) cannot produce these core structures. A copper(I)‐catalyzed interrupted click reaction to access diverse 5‐functionalized triazoles is reported. Various 5‐amino‐, thio‐, and selenotriazoles were readily assembled in one step in high yields. The reaction proceeds under mild conditions with complete regioselectivity. It also features a broad substrate scope and good functional group compatibility.     

A Strategy toward Cyclic Topologies Based on the Dynamic Behavior of a Bis(hindered amino)disulfide Linker

A simple and efficient method to generate macrocyclic structures has been developed based on the dynamic behavior of the linker bis(2,2,6,6‐tetramethylpiperidin‐1‐yl)disulfide (BiTEMPS). The prime linear structure was transformed into a (macro)cycle using the following sequence: 1) thiol–ene reaction with a BiTEMPS derivative to afford the linear precursor, then 2) an entropy‐driven transformation induced by diluting and heating. The radicals generated from BiTEMPS upon heating are highly tolerant toward a variety of chemical species, including oxygen and olefins, but they exhibit high reactivity in exchange reactions, which can be applied to the topology transformation of various skeletons. The advantages of the present method, namely, its procedural simplicity and substrate versatility, are demonstrated by the gram‐scale synthesis of cyclic compounds with low and relatively high molecular weight.     

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding

The hierarchical self‐assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide‐based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error‐check and error‐correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed.     

A Diaminodiacid (DADA) Strategy for the Development of Disulfide Surrogate Peptides

Disulfide bond‐containing peptides are useful molecular scaffolds with diagnostic and therapeutic applications due to their good biological activity and good target selectivity, but their utility is sometimes limited by the lability of the disulfide moiety under reducing conditions and in the presence of disulfide bond isomerase. The development of disulfide surrogates with improved redox stability has been an area of ongoing research; and one possible strategy is based on a diaminodiacid (DADA) moiety, which can be used to synthesize the disulfide bond replacement peptides with precise structures and enhanced stability through automated solid‐phase peptide synthesis (SPPS). This review summarizes recent developments in the DADA‐based SPPS of peptide disulfide surrogates. Some representative applications and structural studies on the DADA‐based disulfide surrogates are described.     

Development of a Terpenoid Alkaloid‐like Compound Library Based on the Humulene Skeleton

Many natural terpenoid alkaloid conjugates show biological activity because their structures contain both sp³‐rich terpenoid scaffolds and nitrogen‐containing alkaloid scaffolds. However, their biosynthesis utilizes a limited set of compounds as sources of the terpenoid moiety. The production of terpenoid alkaloids containing various types of terpenoid moiety may provide useful, chemically diverse compound libraries for drug discovery. Herein, we report the construction of a library of terpenoid alkaloid‐like compounds based on Lewis‐acid‐catalyzed transannulation of humulene diepoxide and subsequent sequential olefin metathesis. Cheminformatic analysis quantitatively showed that the synthesized terpenoid alkaloid‐like compound library has a high level of three‐dimensional‐shape diversity. Extensive pharmacological screening of the library has led to the identification of promising compounds for the development of antihypolipidemic drugs. Therefore, the synthesis of terpenoid alkaloid‐like compound libraries based on humulene is well suited to drug discovery. Synthesis of terpenoid alkaloid‐like compounds based on several natural terpenoids is an effective strategy for producing chemically diverse libraries.     

Chiral Phosphoric Acid Catalyzed Atroposelective C−H Amination of Arenes

N‐arylcarbazole structures are important because of their prevalence in natural products and functional OLED materials. C?H amination of arenes has been widely recognized as the most efficient approach to access these structures. Conventional strategies involving transition‐metal catalysts suffer from confined substrate generality and the requirement of exogenous oxidants. Organocatalytic enantioselective C–N chiral axis construction remains elusive. Presented here is the first organocatalytic strategy for the synthesis of novel axially chiral N‐arylcarbazole frameworks by the assembly of azonaphthalenes and carbazoles. This reaction accommodates broad substrate scope and gives atropisomeric N‐arylcarbazoles in good yields with excellent enantiocontrol. This approach not only offers an alternative to metal‐catalyzed C–N cross‐coupling, but also brings about opportunities for the exploitation of structurally diverse N‐aryl atropisomers and OLED materials.     

Quantum chemistry studies of adenosine 2503 methylation by S‐adenosylmethionine‐dependent enzymes

Ribosome methylation is important for life processes and is mainly catalyzed by radical S‐Adenosylmethionine (SAM) enzymes. Two SAM molecules serve as the cofactor by providing the 5 ′‐deoxyadenosyl radical for substrate activation and the methyl. Recently, Booker and coworkers (Science 2011, 332, 604) proposed an alternative mechanism for a pair of radical SAM enzymes, RlmN and Cfr, which respectively methylate the C2 and C8 of adenosine 2503. Their deuterium labeling experiments reveal that methyl group does not transfer directly from SAM to adenosine, instead it passes to Cys³⁵⁵ first, then onto adenosine. In this article, this new reaction mechanism is studied using density functional theory with B3LYP hybrid functional. The reaction system is simulated using small model compounds in the gas phase, and the protein environment is approximated using polarizable continuum model. The structures of the transition states and the intermediates are identified, and their free energies are calculated. The activation barriers indicate that the proposed reaction mechanism is plausible. The formation of a disulfide bond is found to be the rate‐limiting step. © 2012 Wiley Periodicals, Inc.     

Application of Fragment‐Based Screening to the Design of Inhibitors of Escherichia coli DsbA

The thiol‐disulfide oxidoreductase enzyme DsbA catalyzes the formation of disulfide bonds in the periplasm of Gram‐negative bacteria. DsbA substrates include proteins involved in bacterial virulence. In the absence of DsbA, many of these proteins do not fold correctly, which renders the bacteria avirulent. Thus DsbA is a critical mediator of virulence and inhibitors may act as antivirulence agents. Biophysical screening has been employed to identify fragments that bind to DsbA from Escherichia coli. Elaboration of one of these fragments produced compounds that inhibit DsbA activity in vitro. In cell‐based assays, the compounds inhibit bacterial motility, but have no effect on growth in liquid culture, which is consistent with selective inhibition of DsbA. Crystal structures of inhibitors bound to DsbA indicate that they bind adjacent to the active site. Together, the data suggest that DsbA may be amenable to the development of novel antibacterial compounds that act by inhibiting bacterial virulence.     

Natural‐Product Sugar Biosynthesis and Enzymatic Glycodiversification

Many biologically active small‐molecule natural products produced by microorganisms derive their activities from sugar substituents. Changing the structures of these sugars can have a profound impact on the biological properties of the parent compounds. This realization has inspired attempts to derivatize the sugar moieties of these natural products through exploitation of the sugar biosynthetic machinery. This approach requires an understanding of the biosynthetic pathway of each target sugar and detailed mechanistic knowledge of the key enzymes. Scientists have begun to unravel the biosynthetic logic behind the assembly of many glycosylated natural products and have found that a core set of enzyme activities is mixed and matched to synthesize the diverse sugar structures observed in nature. Remarkably, many of these sugar biosynthetic enzymes and glycosyltransferases also exhibit relaxed substrate specificity. The promiscuity of these enzymes has prompted efforts to modify the sugar structures and alter the glycosylation patterns of natural products through metabolic pathway engineering and enzymatic glycodiversification. In applied biomedical research, these studies will enable the development of new glycosylation tools and generate novel glycoforms of secondary metabolites with useful biological activity.     

Photocontrolled Release of Chemicals from Nano‐ and Microparticle Containers

A benzoin‐derived diol linker was synthesized and used to generate biocompatible polyesters that can be fully decomposed on demand upon UV irradiation. Extensive structural optimization of the linker unit was performed to enable the defined encapsulation of diverse organic compounds in the polymeric structures and allow for a well‐controllable polymer cleavage process. Selective tracking of the release kinetics of encapsulated model compounds from the polymeric nano‐ and microparticle containers was performed by confocal laser scanning microscopy in a proof‐of‐principle study. The physicochemical properties of the incorporated and released model compounds ranged from fully hydrophilic to fully hydrophobic. The demonstrated biocompatibility of the utilized polyesters and degradation products enables their use in advanced applications, for example, for the smart packaging of UV‐sensitive pharmaceuticals, nutritional components, or even in the area of spatially selective self‐healing processes.     

Flexible host frameworks with diverse cavities in inclusion crystals of bile acids and their derivatives

We have systematically investigated structures and properties of inclusion crystals of bile acids and their derivatives. These steroidal compounds form diverse host frameworks having zero‐, one‐ and two‐dimensional cavities, causing various inclusion behaviors towards many organic compounds. The diverse host frameworks exhibit the following guest‐dependent flexibility. First, the frameworks mainly depend on the included guests in size and shape. The size‐dependence is quantitatively estimated by the parameter PCcavity, which is the volume ratio of a guest molecule to a host cavity. The resulting values of PCcavity lie in the range of 42–76%. Second, each of the host frameworks has its own range of the values. Some guests can employ two different frameworks with the boundary values, explaining formation of polymorphic crystals. Third, the host frameworks are selected by host–guest interactions through weak hydrogen bonds, such as NH/π and CH/O. The weak hydrogen bonds play an important role for various selective inclusion processes. Fourth, the host frameworks are dynamically exchangeable, resulting in intercalation and polymerization in the cavities. These static and dynamic structures of the frameworks demonstrate great potential of crystalline organic inclusion compounds as functional materials. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 124–135; 2009: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.20171     

Cleaving Direct‐Laser‐Written Microstructures on Demand

Using an advanced functional photoresist we introduce direct‐laser‐written (DLW) 3D microstructures capable of complete degradation on demand. The networks consist exclusively of reversible bonds, formed by irradiation of a phenacyl sulfide linker, giving disulfide bonds in a radical‐free step‐growth polymerization via a reactive thioaldehyde. The bond formation was verified in solution by ESI‐MS. To induce cleavage, dithiothreitol causes a thiol–disulfide exchange, erasing the written structure. The mild cleavage of the disulfide network is highly orthogonal to other, for example, acrylate‐based DLW structures. To emphasize this aspect, DLW structures were prepared incorporating reversible structural elements into a non‐reversible acrylate‐based standard scaffold, confirming subsequent selective cleavage. The high lateral resolution achievable was verified by the preparation of well‐defined line gratings with line separations of down to 300 nm.     

Reversible Morphological Transformation between Polymer Nanocapsules and Thin Films through Dynamic Covalent Self‐Assembly

A facile method has been developed for synthesizing polymer nanocapsules and thin films using multiple in‐plane stitching of monomers by the formation of reversible disulfide linkages. Owing to the reversibility of the disulfide linkages, the nanostructured materials readily transform their structures in response to environmental changes at room temperature. For example, in reducing environments, the polymer nanocapsules release loaded cargo molecules. Moreover, reversible morphological transformations between these structures can be achieved by simple solvent exchanges. This work is a novel approach for the formation of robust nano/microstructured materials that dynamically respond to environmental stimuli.     

Conformational studies of dammarane‐type triterpenoids using computational and NMR spectroscopic methods

Natural triterpenoids are of great interest to researchers of various fields as they possess diverse physicochemical and biological properties. In medicinal chemistry, detailed information about the chemical structures of bioactive triterpenoids often helps find new lead compounds. Herein, the low‐energy structures of (20S)‐protopanaxadiol and (20S)‐protopanaxatriol, the aglycones of various triterpenoid saponins found in Panax ginseng, and their (20R)‐epimers have been predicted by the geometry optimization of the conformers extracted from molecular dynamics simulations with the self‐consistent‐charge density functional tight‐binding method. By performing quantum mechanical calculations on the low‐energy conformers, we have estimated the NMR chemical shifts of the compounds, which display good agreement with the most recently reported experimental values within an expected range of errors. Our results indicate that theoretical estimation of the NMR parameters of a relatively large molecule with a molecular mass of 500 is feasible. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis of 2‐cyanoacrylates containing pyridinyl moiety under ultrasound irradiation

Reaction of ethyl cyanoacetate with carbon disulfide and dimethyl sulfate in the presence of sodium methoxide in anhydrous methanol yields ethyl 2‐cyano‐3,3‐dimethyl‐ thioacrylate, followed by the nucle‐ophilic substitution with 2‐amino‐3‐chloro‐4‐ methylpyridine under ultrasonic irradiation affording the key intermediate, ethyl 3‐(2‐chloro‐4‐methylpyridin‐3‐ylamino)‐2‐cyano‐3‐methylthioacrylate. The title compounds were then obtained through the reaction of the key intermediate with the aliphatic amine under reflux condition. All the new structures were verified by elemental analysis, IR, ¹H NMR and mass spectra. In the MTT test, these new compounds were found to possess moderate antitumor activities against PC3 and A431 cells.     

Structural Basis for Bulky‐Adduct DNA‐Lesion Recognition by the Nucleotide Excision Repair Protein Rad14

Heterocyclic aromatic amines react with purine bases and result in bulky DNA adducts that cause mutations. Such structurally diverse lesions are substrates for the nucleotide excision repair (NER). It is thought that the NER machinery recognises and verifies distorted DNA conformations, also involving the xeroderma pigmentosum group A and C proteins (XPA, XPC) that act as a scaffold between the DNA substrate and several other NER proteins. Here we present the synthesis of DNA molecules containing the polycyclic, aromatic amine C8‐guanine lesions acetylaminophenyl, acetylaminonaphthyl, acetylaminoanthryl, and acetylaminopyrenyl, as well as their crystal structures in complex with the yeast XPA homologue Rad14. This work further substantiates the indirect lesion‐detection mechanism employed by the NER system that recognises destabilised and deformable DNA structures.     

Synthesis of Some New Heterocycles Derived from Novel 2‐(1,3‐Dioxisoindolin‐2‐yl)Benzoyl Isothiocyanate

Novel 2‐(1,3‐Dioxisoindolin‐2‐yl)benzoyl isothiocyanate was prepared and underwent addition–cyclization reactions with some nucleophilic reagents. Simultaneous or subsequent cyclization of the obtained adducts gave a diverse range of differently sized heterocycles and thioureas. The structures of the synthesized compounds were confirmed by microanalytical and spectral data.     

Racemic and Quasi‐Racemic X‐ray Structures of Cyclic Disulfide‐Rich Peptide Drug Scaffolds

Cyclic disulfide‐rich peptides have exceptional stability and are promising frameworks for drug design. We were interested in obtaining X‐ray structures of these peptides to assist in drug design applications, but disulfide‐rich peptides can be notoriously difficult to crystallize. To overcome this limitation, we chemically synthesized the L ‐ and D ‐forms of three prototypic cyclic disulfide‐rich peptides: SFTI‐1 (14‐mer with one disulfide bond), cVc1.1 (22‐mer with two disulfide bonds), and kB1 (29‐mer with three disulfide bonds) for racemic crystallization studies. Facile crystal formation occurred from a racemic mixture of each peptide, giving structures solved at resolutions from 1.25 Å to 1.9 Å. Additionally, we obtained the quasi‐racemic structures of two mutants of kB1, [G6A]kB1, and [V25A]kB1, which were solved at a resolution of 1.25 Å and 2.3 Å, respectively. The racemic crystallography approach appears to have broad utility in the structural biology of cyclic peptides.     

Diversity Oriented Clicking (DOC): Divergent Synthesis of SuFExable Pharmacophores from 2‐Substituted‐Alkynyl‐1‐Sulfonyl Fluoride (SASF) Hubs

Diversity Oriented Clicking (DOC) is a unified click‐approach for the modular synthesis of lead‐like structures through application of the wide family of click transformations. DOC evolved from the concept of achieving “diversity with ease”, by combining classic C?C π‐bond click chemistry with recent developments in connective SuFEx‐technologies. We showcase 2‐S ubstituted‐A lkynyl‐1‐S ulfonyl F luorides (SASFs) as a new class of connective hub in concert with a diverse selection of click‐cycloaddition processes. Through the selective DOC of SASFs with a range of dipoles and cyclic dienes, we report a diverse click‐library of 173 unique functional molecules in minimal synthetic steps. The SuFExable library comprises 10 discrete heterocyclic core structures derived from 1,3‐ and 1,5‐dipoles; while reaction with cyclic dienes yields several three‐dimensional bicyclic Diels–Alder adducts. Growing the library to 278 discrete compounds through late‐stage modification was made possible through SuFEx click derivatization of the pendant sulfonyl fluoride group in 96 well‐plates—demonstrating the versatility of the DOC approach for the rapid synthesis of diverse functional structures. Screening for function against MRSA (USA300) revealed several lead hits with improved activity over methicillin.     

Selective Dynamic Assembly of Disulfide Macrocyclic Helical Foldamers with Remote Communication of Handedness

Disulfide bridge formation was investigated in helical aromatic oligoamide foldamers. Depending on the position of thiol‐bearing side chains, exclusive intramolecular or intermolecular disulfide bridging may occur. The two processes are capable of self‐sorting, presumably by dynamic exchange. Quantitative assessment of helix handedness inversion rates showed that bridging stabilizes the folded structures. Intermolecular disulfide bridging serendipitously yielded a well‐defined, C₂‐symmetrical, two‐helix bundle‐like macrocyclic structure in which complete control over relative handedness, that is, helix–helix handedness communication, is mediated remotely by the disulfide bridged side chains in the absence of contacts between helices. MM calculations suggest that this phenomenon is specific to a given side chain length and requires disulfide functions