Organic & Biomolecular Chemistry (v.17, #7)

Front cover (1575-1575).

Inside front cover (1576-1576).

Contents list (1577-1594).

Recent advances in homogeneous borrowing hydrogen catalysis using earth-abundant first row transition metals by Benjamin G. Reed-Berendt; Kurt Polidano; Louis C. Morrill (1595-1607).
The review highlights the recent advances (2013-present) in the use of earth-abundant first row transition metals in homogeneous borrowing hydrogen catalysis. The utility of catalysts based on Mn, Fe, Co, Ni and Cu to promote a diverse array of important C–C and C–N bond forming reactions is described, including discussion on reaction mechanisms, scope and limitations, and future challenges in this burgeoning area of sustainable catalysis.

Diversity-oriented synthesis has historically focused on the generation of small-molecule collections with considerable scaffold, stereochemical, and appendage diversity. Recently, this focus has begun to shift to the production of small-molecule libraries with diverse biological activities. It is currently not clear which properties and structural features of molecules are predictive of diverse performance in biological assays, and a better understanding of this relationship is critical for the development of performance-diverse small-molecule libraries for the discovery of novel probes for challenging targets. This review explores recent synthetic strategies for the production of bioactive small molecules and concludes with a presentation of current methods that enable the assessment of the biological performance diversity of small-molecule libraries.

Rearranged ergostane-type natural products: chemistry, biology, and medicinal aspects by Fenja L. Duecker; Franziska Reuß; Philipp Heretsch (1624-1633).
Classical steroids are long-known privileged leads in drug discovery. Their rearranged counterparts, though, have so far received less attention, although recent isolation and biological testing programmes have revealed a plethora of molecular entities that are both structurally intriguing, as well as biologically relevant. This review will highlight those natural products, and focus on ergostane-derived seco- and abeo-steroids. Their isolation, structure elucidation, and biological properties are reported. A special emphasis of this review lies in their respective (and typically proposed) biosyntheses, to help guide future bio-inspired synthetic attempts.

The challenge of using isopropylamine as an amine donor in transaminase catalysed reactions by Panagiotis Kelefiotis-Stratidakis; Theodore Tyrikos-Ergas; Ioannis V. Pavlidis (1634-1642).
Amine transaminases (ATAs) propose an appealing alternative to transition metal catalysts as they can provide chiral amines of high purity from pro-chiral compounds by asymmetric synthesis. Industrial interest on ATAs arises from the fact that chiral amines are present in a wide spectrum of pharmaceutical and other high value-added chiral compounds and building blocks. Despite their potential as useful synthetic tools, several drawbacks such as challenges associated with the thermodynamic equilibrium can still impede their utilization. Several methods have been developed to displace the equilibrium, such as the use of alanine as an amine donor and the subsequent removal of pyruvate with a two-enzyme system, or the use of o-xylylene diamine. To date, the preferred amine donor remains isopropylamine (IPA), as the produced acetone can be removed easily under low pressure or slight heating, without complicating the process with other enzymes. Despite its small size, IPA is not widely accepted from wild-type ATAs, and this fact compromises its wide applicability. Herein, we index the reported biocatalytic aminations with IPA, comparing the sequences, while we discuss significant parameters of the process, such as the effect of temperature and pH, as well as the protein engineering and process development advances in the field. This information is expected to provide an insight for potential designs of tailor-made ATAs and IPA processes.

Intermolecular alkene difunctionalizations for the synthesis of saturated heterocycles by Navdeep Kaur; Fan Wu; Nur-E Alom; Jeewani P. Ariyarathna; Shannon J. Saluga; Wei Li (1643-1654).
Saturated heterocycles are important structural motifs in a range of pharmaceuticals and agrochemicals. As a result of their importance, syntheses of these molecules have been extensively investigated. Despite the progress in this area, the most adopted strategies are still often characterized with inefficiency or relying on functionalizations with specialized precursors and pre-existing cores. This review highlights a dynamic synthetic strategy for the direct synthesis of saturated heterocycles from intermolecular alkene difunctionalizations. These coupling processes are highly modular, and therefore, offer perhaps the most convenient means to prepare diverse heterocyclic structures in compound libraries for bioactivity evoluations.

Beyond the traditional roles of Ag in catalysis: the transmetalating ability of organosilver(i) species in Pd-catalysed reactions by Ángel L. Mudarra; Sara Martínez de Salinas; Mónica H. Pérez-Temprano (1655-1667).
Silver salts are one of the most widely used additives in Pd-catalysed transformations. Apart from acting as a halide scavenger and/or an external oxidant, over the past decade it has been revealed that silver salts can play other roles such as a C–H activation promoter or decarboxylating agent, generating organosilver(i) species. These nucleophiles can promote innovative transformations by reacting with PdII intermediates through a transmetalation step. This review article covers different Pd-catalysed C–C bond-forming reactions where silver complexes have been proposed to act as nucleophilic coupling partners. We will also provide relevant mechanistic features associated with these transformations.

Peptide–oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.

In recent years, a renewal of interest was shown to the quest for new synthetic solutions to directly introduce emergent fluorinated groups (SRf) onto molecules. In this context, a new generation of reagents (ArSO2SRf) as efficient sources of SCF3, SCF2H and more generally SRf groups, was designed. Hence, potent solutions were developed for the synthesis of SRf-containing molecules, compounds of interest for drug and agrochemical research. This review highlights the recent advances made in the synthesis and the use of this new class of reagents, considerably extending the portfolio of tools for the direct introduction of SRf moieties.

The first construction of the challenging β-(1 → 5)-linked GalNAc-Kdo skeleton is described for the synthesis of the disaccharide antigen of the capsular polysaccharide of Kingella kingae KK01. TfOH-catalyzed glycosylation of N-Troc-protected d-galactosaminyl N-phenyl trifluoroacetimidate with a sterically hindered 5-hydroxyl group of the β-Kdo building block in toluene proceeded smoothly to provide the desired disaccharide in excellent yield with satisfactory β-selectivity. An optimal sequence for the deprotection of the disaccharide skeleton was found to access the disaccharide antigen of Kingella kingae KK01 for further immunological studies.

Total synthesis of incargranine A by Patrick D. Brown; Andrew L. Lawrence (1698-1702).
Synthetic studies into the origins of the alkaloid incargranine A have resulted in the development of a four-step (longest linear sequence) total synthesis. This synthesis has been scaled-up to provide gram-scale quantities of material, which would alternatively require extraction of several metric-tons of dried-whole Chinese Trumpet-Creeper plants (Incarvillea mairei var. grandiflora).

Synthesis of hydrophobic insulin-based peptides using a helping hand strategy by Maria M. Disotuar; Mark E. Petersen; Jason M. Nogueira; Michael S. Kay; Danny Hung-Chieh Chou (1703-1708).
The introduction of solid-phase peptide synthesis in the 1960s improved the chemical synthesis of both the A- and B-chains of insulin and insulin analogs. However, the subsequent elaboration of the synthetic peptides to generate active hormones continues to be difficult and complex due in part to the hydrophobicity of the A-chain. Over the past decade, several groups have developed different methods to enhance A-chain solubility. Two of the most popular methods are use of isoacyl dipeptides, and the attachment of an A-chain C-terminal pentalysine tag with a base-labile 4-hydroxymethylbenzoic acid linker. These methods have proven effective but can be limited in scope depending on the peptide sequence of a specific insulin. Herein we describe an auxiliary approach to enhance the solubility of insulin-based peptides by incorporating a tri-lysine tag attached to a cleavable Fmoc-Ddae-OH linker. Incorporation of this linker, or “helping hand”, on the N-terminus greatly improved the solubility of chicken insulin A-chain, which is analogous to human insulin, and allowed for coupling of the insulin A- and B-chain via directed disulfide bond formation. After formation of the insulin heterodimer, the linker and tag could be easily removed using a hydrazine buffer (pH 7.5) to obtain an overall 12.6% yield based on A-chain. This strategy offers an efficient method to enhance the solubility of hydrophobic insulin-based peptides as well as other traditionally difficult peptides.

Palladium-catalyzed salt-free double decarboxylative aryl allylation by Ryan A. Daley; Joseph J. Topczewski (1709-1713).
This report describes a palladium-catalyzed decarboxylative aryl allylation between unactivated benzoic acids and allylic carbonates. This transformation successfully couples a variety of carbonates and benzoic acids in good yield (up to 94%) using 1 mol% palladium. This salt free allyl-arylation proceeds without added base, copper, or silver. The only stoichiometric byproducts are carbon dioxide and tert-butanol.

Highly regioselective α-alkylation of α,β,γ,δ-unsaturated aldehydes by Venkata M. D. Padmaja; Sachin Jangra; Chandrakumar Appayee (1714-1717).
The first α-alkylation of α,β,γ,δ-unsaturated aldehydes is achieved under mild reaction conditions. Several α,β,γ,δ-unsaturated aldehydes and diarylcarbinols are successfully tested for the synthesis of MBH-type α-alkylated products with an excellent regioselectivity. Simple pyrrolidine is efficiently used as a catalyst to achieve a perfect E/Z selectivity of the α-alkylated products.

An organocatalytic asymmetric cascade Michael/hemiketalization/acyl transfer reaction between (E)-2-(2-nitrovinyl)phenols and 1,3-propanediones is disclosed. A cinchona alkaloid derived bifunctional thiourea catalyst was found to be the most effective for this reaction and provided the desired products in moderate to good yields with good to high enantioselectivities.

Robust Buchwald–Hartwig amination enabled by ball-milling by Qun Cao; William I. Nicholson; Andrew C. Jones; Duncan L. Browne (1722-1726).
An operationally simple mechanochemical method for the Pd catalysed Buchwald–Hartwig amination of arylhalides with secondary amines has been developed using a Pd PEPPSI catalyst system. The system is demonstrated on 30 substrates and applied in the context of a target synthesis. Furthermore, the performance of the reaction under aerobic conditions has been probed under traditional solution and mechanochemical conditions, the observations are discussed herein.

Synthesis of the core structure of phalarine by Kazuya Douki; Jun Shimokawa; Masato Kitamura (1727-1730).
The core skeleton of phalarine was rapidly synthesised through novel palladium-catalysed dearomative spirocyclisation and a palladium-catalysed Wacker-carbonylative cyclisation cascade. The two key steps allowed for the efficient construction of a tricyclic propeller skeleton bearing contiguous tetrasubstituted carbon centres, within 3 steps from a topologically planar precursor.

Palladium-catalyzed intramolecular carboborylation of 1,3-diene and synthesis of ABCD ring of communesins by Chihiro Tsukano; Motoyuki Nakajima; Sudhir M. Hande; Yoshiji Takemoto (1731-1735).
A palladium-catalyzed intramolecular carboborylation of 1,3-diene has been developed for the synthesis of iminoindolines with a quaternary carbon centre. This method was applied to a substrate bearing several functional groups to afford a complex iminoindoline, which was subsequently converted into an ABCD ring model compound of communesins via an intramolecular Friedel–Crafts-type reaction.

We present the functional characterization of GlbB, a lysine 4-hydroxylase from the glidobactin biosynthetic gene cluster. Despite its narrow substrate specificity, GlbB is able to catalyze the hydroxylation of l-lysine with excellent total turnover number and complete regio- and diastereoselectivity. The synthetic utility of GlbB is illustrated by its use in the efficient preparation of a key dipeptide fragment of glidobactin.

A one-pot oxidative cross-dehydrogenative [2 + 3] annulation of α-amino ketones with α-keto esters at room temperature is reported. The protocol features copper/organo cooperative catalysis and provides densely functionalized pyrrolones in high yields. Subsequent reduction furnished multi-substituted pyrrolidinones which represent the core-structure of the natural product clausenamide, a lead molecule for the treatment of Alzheimer's disease.

Selective alkyl ether cleavage by cationic bis(phosphine)iridium complexes by Caleb A. H. Jones; Nathan D. Schley (1744-1748).
Catalysts capable of heterolytic silane activation have been successfully applied to the conversion of alkyl ethers to silyl ethers via C–O bond cleavage. The previously-reported cationic pincer-supported iridium complex for this transformation suffers from poor selectivity with regard to monodealkylation of substrate ethers. We demonstrate that a simple non-pincer iridium complex offers improved selectivity and is capable of benzylic ether cleavage in the presence of reductively-labile alkyl and aryl halide functionality. Preliminary mechanistic experiments suggest a neutral tetrahydridosilyliridium resting state which is consistent with previous mechanistic hypotheses. These experiments suggest that a pincer ligand framework is not required for activity in ether cleavage reactions and that simple cationic bis(phosphine)iridium complexes may offer improved selectivity profiles for applications to more-complex substrate molecules.

Iron-catalyzed protodehalogenation of alkyl and aryl halides using hydrosilanes by Ramadevi Pilli; Venkadesh Balakrishnan; Revathi Chandrasekaran; Ramesh Rasappan (1749-1753).
A simple and efficient iron-catalyzed protodehalogenation of alkyl and aryl halides using phenylhydrosilane is disclosed. The reaction utilizes FeCl3 without the requirement of ligands. Unactivated alkyl and aryl halides were successfully reduced in good yields; sterically hindered tertiary halides were also reduced including the less reactive chlorides. The scalability of this methodology was demonstrated by a gram-scale synthesis with a catalyst loading as low as 0.5 mol%. Notably, disproportionation of phenylsilane leads to diphenylsilane that further reduces the halides. Preliminary mechanistic studies revealed a non-radical pathway and the source of hydrogen is PhSiH3via deuterium labeling studies. Our methodology represents simplicity and provides a good alternative to typical tin, aluminum and boron hydride reagents.

Total synthesis of (±)-antroquinonol by Xiaoming Wang; Chao Du; Benke Hong; Xiaoguang Lei (1754-1757).
We report the total synthesis of (±)-antroquinonol based on a concise and efficient route. Key features include two different strategies to install the required three contiguous stereogenic centers, which not only furnish the desired natural product but also provide natural product congeners for further biological studies.

Synthesis of fluoroalkylated alkynes via visible-light photocatalysis by Naila Iqbal; Naeem Iqbal; Sung Su Han; Eun Jin Cho (1758-1762).
Fluoroalkylated alkynes, which are versatile building blocks for the synthesis of various biologically active organofluorine compounds, were synthesized from easily available alkynyl halides and fluoroalkyl halides by visible-light photocatalysis. Addition of fluoroalkyl radicals to alkynes and subsequent dehalogenation selectively yielded fluoroalkylated alkynes.

Chiral selenide-catalyzed enantioselective synthesis of trifluoromethylthiolated 2,5-disubstituted oxazolines by Tian Qin; Quanbin Jiang; Jieying Ji; Jie Luo; Xiaodan Zhao (1763-1766).
Chiral selenide-catalyzed enantioselective trifluoromethylthiolation of 1,1-disubstituted alkenes is disclosed. By this method, a variety of chiral trifluoromethylthiolated 2,5-disubstituted oxazolines were obtained in good yields with high enantioselectivities. This work not only provides a new pathway for the synthesis of chiral oxazolines, but also expands the library of chiral trifluoromethylthiolated molecules.

Mechanism of nitrones and allenoates cascade reactions for the synthesis of dihydro[1,2-a]indoles by Wes Lee; Mingbin Yuan; Christopher Acha; Ashley Onwu; Osvaldo Gutierrez (1767-1772).
Quantum mechanical calculations (DLPNO-CCSD(T) and dispersion-corrected DFT) are employed to gain insights into the mechanism and selectivity in the catalytic synthesis of dihydropyrido[1,2-a]indoles from the cascade reaction between nitrones and allenes. Implications for controlling diverging pathways is discussed.

Multicomponent dipolar cycloadditions: efficient synthesis of polycyclic fused pyrrolizidines via azomethine ylides by Srinivas Samala; Do Hyun Ryu; Choong Eui Song; Eun Jeong Yoo (1773-1777).
An efficient multicomponent dipolar cycloaddition for the synthesis of polycyclic fused pyrrolizidines was developed using N-aromatic zwitterions, aldehydes, and amino acids. The developed reactions proceed through azomethine ylides generated in situ from the decarboxylated reactions of aldehydes and amino acids followed by the [3 + 2] cycloaddition of N-aromatic zwitterions under mild reaction conditions.

Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA by Neeraj N. Patwardhan; Zhengguo Cai; Colby N. Newson; Amanda E. Hargrove (1778-1786).
A prominent hurdle in developing small molecule probes against RNA is the relative scarcity of general screening methods. In this study, we demonstrate the application of a fluorescent peptide displacement assay to screen small molecule probes against four different RNA targets. The designed experimental protocol combined with statistical analysis provides a fast and convenient method to simultaneously evaluate small molecule libraries against different RNA targets and classify them based on affinity and selectivity patterns.

An enantioselective synthesis of α-alkylated pyrroles via cooperative isothiourea/palladium catalysis by W. Rush Scaggs; Toya D. Scaggs; Thomas N. Snaddon (1787-1790).
Herein we describe the direct enantioselective Lewis base/Pd catalysed α-allylation of pyrrole acetic acid esters. This provides high isolated yields of highly enantioenriched products and exhibits broad reaction scope with respect to both reaction partners. The products can be readily elaborated in a manner which points towards potential applications in target directed synthesis.

Copper-catalyzed arene amination in pure aqueous ammonia by Mio Takagi; Ayako Watanabe; Shigeo Murata; Ryo Takita (1791-1795).
A simple protocol for copper-catalyzed arene amination using aqueous ammonia without any additional ligands and organic coordinating solvents has been developed. The reaction pathway via a Cu(i)/Cu(iii) mechanism is proposed based on the results of control experiments as well as DFT calculations.

An alternative protocol for the B-alkyl Suzuki–Miyaura reaction to produce cyclic α,β-disubstituted enones is reported. The use of β-triflyl enones as coupling partners in lieu of their halogenated analogs provides enhanced substrate stability to light and chromatography without adversely affecting reactivity. This protocol allows efficient access to the synthetically challenging α,β-disubstituted enone motif under mild conditions.

An unprecedented method for the direct arylation and heteroarylation of tetrahydroisoquinolines under metal and oxidant free conditions is reported. The arylation reactions occurred via a C(sp3)–H functionalization enabled three component condensation of tetrahydroisoquinolines, 9-fluorenone imine, and arenes without involving a pre-functionalization/pre-derivatization step. A wide range of arenes and heteroarenes participated in the reaction to provide structurally diverse arylated tetrahydroisoquinolines with good to excellent yields.

Posttranscriptional spin labeling of RNA by tetrazine-based cycloaddition by Christof Domnick; Gregor Hagelueken; Frank Eggert; Olav Schiemann; Stephanie Kath-Schorr (1805-1808).
The site-specific introduction of spin labels into RNA for distance measurements by EPR gives insight into its solution structure. We here present a method for spin labeling of in vitro transcribed RNA. Distance distributions between two nitroxide spin labels are determined by PELDOR in a self-complementary RNA duplex.

Radical SAM-dependent adenosylation catalyzed by l-tyrosine lyases by Yujie Wu; Runze Wu; Dhanaraju Mandalapu; Xinjian Ji; Tuo Chen; Wei Ding; Qi Zhang (1809-1812).
The radical S-adenosylmethionine (SAM) superfamily is currently the largest known enzyme family. These enzymes reductively cleave SAM to produce a highly reactive 5′-deoxyadenosyl (dAdo) radical, which abstracts a hydrogen from the substrate and initiates diverse reactions. The canonic dAdo radical-mediated hydrogen abstraction can be changed to radical addition reactions by using olefin-containing substrate analogues, which result in adenosylation reactions. Here we report investigation of the adenosylation reactions catalyzed by four radical SAM l-Tyr lyases (RSTLs), including HydG, FbiC, and two ThiH enzymes from different organisms. We show RSTLs have diverse substrate specificity, and ThiH from E. coli exhibits the highest substrate tolerance toward the tested substrates. We also show ThiH from Clostridium berjerinckii does not act on 4-amino-l-phenylalanine, but catalyzes adenosylation of the corresponding olefin-containing analogue, suggesting adenosylation may occur more easily than the canonic radical SAM reactions. Our study highlights the remarkable catalytic promiscuity of radical SAM enzyme and the potential in using these enzymes for the synthesis of nucleotide-containing compounds.

A fluorogenic C4N4 probe for azide-based labelling by Hidetoshi Noda; Yasuko Asada; Masakatsu Shibasaki; Naoya Kumagai (1813-1816).
The design, synthesis and photophysical properties of a new fluorogenic probe are described. The structure is based on the recently identified 2,5-diaminopyrimidine (C4N4) fluorophore. The strain-promoted [3 + 2] cycloaddition of the azido-C4N4 probe furnished a triazole that exhibited more than 30-fold enhancement in fluorescence intensity as compared to the azide.

Using automated glycan assembly (AGA) for the practical synthesis of heparan sulfate oligosaccharide precursors by Darshita Budhadev; Karinna Saxby; Julia Walton; Gideon Davies; Peter C. Tyler; Ralf Schwörer; Martin A. Fascione (1817-1821).
Herein we report synthesis of complex heparan sulfate oligosaccharide precursors by automated glycan assembly using disaccharide donor building blocks. Rapid access to a hexasaccharide was achieved through iterative solid phase glycosylations on a photolabile resin using Glyconeer™, an automated oligosaccharide synthesiser, followed by photochemical cleavage and glycan purification using simple flash column chromatography.

Formal [4 + 2] benzannulation of 2-alkenyl indoles with aldehydes: a route to structurally diverse carbazoles and bis-carbazoles by Ankush Banerjee; Avishek Guin; Shuvendu Saha; Anushree Mondal; Modhu Sudan Maji (1822-1826).
Construction of structurally diverse carbazoles and bis-carbazoles by protecting-group-free formal [4 + 2]-benzannulation of 2-alkenyl indoles and aldehydes is demonstrated. The sequence of four different reactions is executed in one-pot using readily available and cheap bottle reagents as catalysts rendering this method attractive. The incorporation of inexpensive and environmentally benign molecular oxygen as the oxidant into the final aromatization step enables tolerance of several functional groups.

ortho-Fluoroazobenzene derivatives as DNA intercalators for photocontrol of DNA and nucleosome binding by visible light by Benedikt Heinrich; Karim Bouazoune; Matthias Wojcik; Udo Bakowsky; Olalla Vázquez (1827-1833).
We report a high-affinity photoswitchable DNA binder, which displays different nucleosome-binding capacities upon visible-light irradiation. Both photochemical and DNA-recognition properties were examined by UV-Vis, HPLC, CD spectroscopy, NMR, FID assays, EMSA and DLS. Our probe sets the basis for developing new optoepigenetic tools for conditional modulation of nucleosomal DNA accessibility.

Iron catalysed selective reduction of esters to alcohols by Sem Raj Tamang; Anthony F. Cozzolino; Michael Findlater (1834-1838).
The reaction of (dppBIAN)FeCl2 with 3 equivalents of n-BuLi affords a catalytically active anionic Fe complex; the nature of the anionic complex was probed using EPR and IR experiments and is proposed to involve a dearomatized, radical, ligand scaffold. This complex is an active catalyst for the hydrosilylation of esters to afford alcohols; loadings as low as 1 mol% were employed.

Photoinduced decarboxylative azidation of cyclic amino acids by David C. Marcote; Rosie Street-Jeakings; Elizabeth Dauncey; James J. Douglas; Alessandro Ruffoni; Daniele Leonori (1839-1842).
The direct decarboxylative azidation of cyclic α-amino acids has been achieved via visible light-mediated organo-photoredox catalysis. This synthetic strategy allows the simple preparation of azide-contaning building blocks and has been used in the selective modification of N-terminal proline residues of two di-peptides.

Methyl 5-MeO-N-aminoanthranilate, a minimalist fluorogenic probe for sensing cellular aldehydic load by Mojmír Suchý; Caitlin Lazurko; Alexia Kirby; Trina Dang; George Liu; Adam J. Shuhendler (1843-1853).
Methyl 5-MeO-N-aminoanthranilate, a fluorogenic probe comprising a single substituted benzene ring has been applied towards the fluorescence detection of endogenous carbonyls through rapid, catalyst-free complexation of these bio-derived markers of cell stress under physiological conditions. The products formed during the reaction between the probe and aldehydic products of lipid peroxidation, including malondialdehyde and long-chain aliphatic aldehydes relevant to the oxidative decomposition of cell membranes, have been evaluated. Live cell imaging of diethyl maleate-induced oxidative stress with or without pretreatment with α-tocopherol was carried out, with the result suggesting that the presented molecule might serve as a minimalist molecular probe capable of cellular “Aldehydic Load” detection by fluorescence microscopy. This work also outlines functional constraints of the fluorogenic probe (i.e. intramolecular cyclization), providing a realistic evaluation of methyl 5-MeO-N-aminoanthranilate for fluorescence-based aldehyde detection.

A mild and operationally simple methodology is reported for the synthesis of cyclobutane rings imbedded within a C2-symmetric tricyclic framework. The method uses visible light and an iridium-based photocatalyst to drive the oft-stated “forbidden” thermal [2 + 2] cycloaddition of cycloheptenes and analogs. Importantly, it generates cyclobutane with four new stereocenters with excellent stereoselectivity, and perfect regioselectivity. The reaction is propelled forward when the photocatalyst absorbs a visible light photon, which transfers this energy to the cycloheptene. Key to success is, upon excitation to the triplet via sensitization from the photocatalyst, the double bond isomerizes to give the transient, highly strained, trans-cycloheptene. The trans-cycloheptene undergoes a strain relieving thermal, intermolecular [π2s + π2a] cycloaddition with another cis-cycloheptene. X-ray analysis reveals that the major product is the head-to-head, C2-symmetric all trans-cyclobutane. Additionally, a dramatic display structural complexity enhancement is observed with the use of chiral cycloheptenols possessing one stereocenter, which results in the formation of cyclobutanes with six contiguous stereocenters with good to excellent diastereocontrol, and can be used to isolate single stereoisomers of stereochemically complex cyclobutanes in good yield.

Studies on a landscape of perfluoroaromatic-reactive peptides by Ethan D. Evans; Bradley L. Pentelute (1862-1868).
We investigated 26 midsized peptides (∼30 amino acids in length) selected using mRNA display to perform a nucleophilic aromatic substitution reaction (SNAr). Analysis suggested a diverse set of reactive sequences with significant differences in primary sequence, secondary structure and even predicted tertiary structural features. Several of the sequences displayed rapid kinetics allowing for near complete labeling in under one hour. Rosetta ab initio structure prediction of these sequences suggested a landscape of structural features, ranging from beta-sheet-based sequences to those possessing more alpha-helical-like character. Circular dichroism spectroscopy confirmed elements of the structure predictions for the majority of peptides. This analysis additionally uncovered that several peptides underwent secondary structure alterations upon reaction. These results suggest a broad sequence and structural landscape of SNAr active peptides along with a potentially important feature of these biopolymers.

Design, synthesis, and biological evaluation of C7-functionalized DMXAA derivatives as potential human-STING agonists by Jihyun Hwang; Taeho Kang; Janghyun Lee; Byong-Seok Choi; Sunkyu Han (1869-1874).
STING, a central protein in the innate immune response to cytosolic DNA, has emerged as a hot target for the development of vaccine-adjuvants and anticancer drugs. The discovery of potent human-STING (hSTING) agonist is expected to revolutionize the current cancer immunotherapy. Inspired by the X-ray crystal structure of DMXAA (5,6-dimethylxanthenone-4-acetic acid) and hSTINGG230I complex, we designed various DMXAA derivatives that contain a hydrogen bonding donor/acceptor or a halide at the C7 position. While 7-bromo- and 7-hydroxyl-DMXAA showed notable binding to mouse-STING (mSTING), our newly synthesized C7-functionalized DMXAA derivatives did not bind to hSTING. Nevertheless, our newly developed synthetic protocol for the C7-functionalization of DMXAA would be applicable to access other C7-substituted DMXAA analogues as potential hSTING agonists.

Peroxynitrite (ONOO) is involved in a variety of physiological and pathological processes. We designed and synthesized a fluorescent probe SiNH based on Si-rhodamine. The nanoprobe SiNH encapsulated within the amphiphilic copolymer exhibited fast response within 10 s, and it was highly specific for ONOO in aqueous solution. It is demonstrated that the nanoprobe SiNH is applicable for real-time tracing of endogenous ONOO in living cells.

Density functional theory computations and block-localized wavefunction analyses for 57 hydrogen-bonded base pairs document excellent linear correlation between the gas-phase association energies and the degree of aromaticity gain of paired bases (r = 0.949), challenging prevailing views of factors that underlie the proposed electronic complementarity of A·T(U) and G·C base pairs. Base pairing interactions can polarize the π-electrons of interacting bases to increase (or decrease) cyclic 4n + 2π electron delocalization, resulting in aromaticity gain (or loss) in the paired bases, and become strengthened (or weakened). The potential implications of this reciprocal relationship for improving nucleic acid force-fields and for designing robust unnatural base pairs are discussed.

The [6,5,5] tricyclic fungal metabolite galiellalactone is a Michael acceptor that has been demonstrated to be a covalent inhibitor for Signal Transducer and Activator of Transcription 3 (STAT3). Recognizing the ring strain associated with the skeleton of this natural product, we utilized 1R-5S-bicyclo[3.1.0]hexan-2-one as the starting material and developed two novel approaches to accomplish the enantioselective total synthesis of the C4 epimer of galiellalactone in 5 and 7 steps, respectively, which capitalized on an efficient radical cyclization/fragmentation cascade reaction. Furthermore, an activity-based probe of 4-epi-galiellalactone with a terminal alkyne tag was successfully prepared to enable the experiments of activity-based protein profiling (ABPP). Through western blot and proteomic analysis, we not only confirmed the known target STAT3, but also identified a new target protein ataxin-7, which formed a covalent bond with the probe in intact cells via the Cys-129 residue.

Sialylated variants of lacto-N-tetraose exhibit antimicrobial activity against Group B Streptococcus by Kelly M. Craft; Harrison C. Thomas; Steven D. Townsend (1893-1900).
Human milk oligosaccharides (HMOs) possess antimicrobial activity against a number of bacterial pathogens. HMOs prevent infection by serving as decoy receptors that competitively bind pathogens thus preventing pathogen attachment to host epithelial cell receptors. In a second mechanistic pathway, we recently demonstrated that heterogenous HMO extracts exert antimicrobial action against Group B Streptococcus by increasing cellular permeability. As human milk contains ca. 200 unique glycans however, our understanding of which pharmacophores are most important to HMO antimicrobial activity remains immature. In the present study, we describe the first evaluation of the antimicrobial and antibiofilm activities of five structurally defined, ubiquitous sialylated HMOs against Group B Streptococcus.

In this protocol we described a boronic acid-catalysed C-3 selective ring opening of 3,4-epoxy alcohols with thiophenols and thiols as nucleophiles. This diastereo- and enantiospecific reaction provides an efficient entry to prepare a variety of hydroxyl sulfides. Through the directing effect of the hydroxyl group, nucleophilic attack on the C-3 position of the epoxide moiety is favoured. It can be rationalized in a proposed transition state, in which the boronic acid catalyst tethers both epoxides and S-nucleophiles.

A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede by Kwan Ho Jung; Matthew Fares; Leeann S. Grainger; Charles H. Wolstenholme; Anna Hou; Yu Liu; Xin Zhang (1906-1915).
Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M−1 s−1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.

As a privileged chiral scaffold, cinchona alkaloid and its derivatives have reached remarkable success in catalytic asymmetric organic synthesis. In addition to the wide applications of point chirality control, Smith and co-workers recently discovered a quinidine-derived ammonium cation-catalyzed O-alkylation of tetralones, providing an effective approach for the synthesis of axially chiral biaryls. Using density functional theory (DFT) calculations, we studied the reaction mechanism and origins of enantioselectivity of this novel transformation. A stepwise strategy is adopted to ensure efficient and thorough exploration of the massive conformational space of transition state. Our computations suggested that enolate oxygen forms two hydrogen bonds with the chiral ammonium catalyst, and the non-covalent interactions between the cationic benzylic fragment and the methoxy group of enolate plays a critical role in determining the enantioselectivity.

A one-pot, regiospecific synthesis of dihydrofurans bearing a quaternary centre and tetrasubstituted furans is developed from the formal [3 + 2] annulation of tert-propargyl alcohols and 1,3-diketones under Ca(ii)/DBU conditions. The reaction proceeds through the SN2I mechanism to form homoallenyl ketone and a subsequent cycloisomerization to yield novel and new chemical entities of privileged scaffolds.

Sulfur polymer composites as controlled-release fertilisers by Maximilian Mann; Jessica E. Kruger; Firas Andari; Joshua McErlean; Jason R. Gascooke; Jessica A. Smith; Max J. H. Worthington; Cheylan C. C. McKinley; Jonathan A. Campbell; David A. Lewis; Tom Hasell; Michael V. Perkins; Justin M. Chalker (1929-1936).
Sulfur polymer composites were prepared by the reaction of canola oil and elemental sulfur in the presence of the NPK fertiliser components ammonium sulfate, calcium hydrogen phosphate, and potassium chloride. These composites released nutrients in a controlled fashion, resulting in less wasted fertiliser and better health for potted tomato plants when compared to free NPK.

Rh-Catalyzed diastereoselective desymmetrization of enone tethered-cyclohexadienones via tandem arylative cyclization by Sandip B. Jadhav; Satish B. Thopate; Jagadeesh Babu Nanubolu; Rambabu Chegondi (1937-1946).
The rhodium-catalyzed arylative cyclization of enone tethered-cyclohexadienones has been developed with high efficiency, thus providing cis-fused bicyclic enones in good yields and with excellent diastereoselectivities. Furthermore, this mild transformation has a broad range of substrate scope and excellent functional group tolerance. In addition, bicyclic products have an enone functionality, which can be a synthetically valuable handle for further transformations.

Reversibly photoswitchable alkoxy azobenzenes connected benzenetricarboxamide discotic liquid crystals with perpetual long range columnar assembly by Sudha Devi; Indu Bala; Santosh Prasad Gupta; Pravesh Kumar; Santanu Kumar Pal; Sugumar Venkataramani (1947-1954).
Liquid crystals (LCs) with photoswitchable groups are very interesting owing to their dual applications. In this regard, we report the synthesis of long chain alkoxy azobenzene incorporated benzenetricarboxamides 7a–c based room temperature columnar LCs. Apart from the light induced isomerization in the solution phase, the salient feature of these systems is the reversible photoisomerization even in the bulk state with perpetual columnar self-assembly at room temperature. Based on the observation of mesomorphic textures under polarised optical microscopy (POM) and grazing incidence small/wide angle X-ray scattering (GISAXS/GIWAXS) studies, the columnar assembly was found to be stable upon photoisomerization. However, subtle changes in height profile have been observed in AFM measurements after photoswitching. Interestingly, a temperature dependent change between rectangular and hexagonal mesophases in 7a has been observed. Upon extending the alkoxy chain length, only the hexagonal mesophase was observed. For comparison, the corresponding N-methylated derivative of 7a has also been synthesized. Despite the better photoswitching behaviour, due to the lack of planarity and H-bonding, 8a did not show any columnar mesophase.

Metal-free photocatalytic thiol–ene/thiol–yne reactions by Sarbjeet Kaur; Gaoyuan Zhao; Evan Busch; Ting Wang (1955-1961).
The organic photocatalyst (9-mesityl-10-methylacridinum tetrafluoroborate) in the presence of visible light is used to initiate thiol–ene and thiol–yne reactions. Thiyl radicals are generated upon quenching the photoexcited catalyst with a range of thiols. The highlighted mild nature of the reaction conditions allows a broad substrate scope of the reactants. Relying on this efficient metal-free condition, both thiol–ene and thiol–yne reactions between carbohydrates and peptides could be realized in excellent yields.

Ligase-catalyzed oligonucleotide polymerisations (LOOPER) can readily generate libraries of diversely-modified nucleic acid polymers, which can be subjected to iterative rounds of in vitro selection to evolve functional activity. While there exist several different DNA ligases, T4 DNA ligase has most often been used for the process. Recently, T3 DNA ligase was shown to be effective in LOOPER; however, little is known about the fidelity and efficiency of this enzyme in LOOPER. In this paper we evaluate the efficiency of T3 DNA ligase and T4 DNA ligase for various codon lengths and compositions within the context of polymerisation fidelity and yield. We find that T3 DNA ligase exhibits high efficiency and fidelity with short codon lengths, but struggles with longer and more complex codon libraries, while T4 DNA ligase exhibits the opposite trend. Interestingly, T3 DNA ligase is unable to accommodate modifications at the 8-position of adenosine when integrated into short codons, which will create challenges in expanding the available codon set for the process. The limitations and strengths of the two ligases are further discussed within the context of LOOPER.

Synthesis and initial biological evaluation of myxocoumarin B by Jonas I. Müller; Kalina Kusserow; Gesa Hertrampf; Aleksandar Pavic; Jasmina Nikodinovic-Runic; Tobias A. M. Gulder (1966-1969).
The myxocoumarins A and B from Stigmatella aurantiaca MYX-030 are natural products featuring unusual nitro- and long-chain alkyl substitution. While myxocoumarin A was shown to exhibit strong antifungal properties, the antifungal potential of myxocoumarin B was not yet assessed due to low production titers during initial isolation. We therefore developed a total synthesis of myxocoumarin B that involves a late-stage Pd-catalyzed nitration of the coumarin core. The availability of synthetic material facilitated the initial evaluation of the bioactivity of myxocoumarin B, which revealed a lack of activity against medically relevant Candida sp. and low cytotoxicity in vitro against human fibroblasts (MRC-5) and in vivo (zebrafish).

Chemoselective reduction of isothiocyanates to thioformamides mediated by the Schwartz reagent by Karen de la Vega-Hernández; Raffaele Senatore; Margherita Miele; Ernst Urban; Wolfgang Holzer; Vittorio Pace (1970-1978).
Thioformamides are easily prepared – under full chemocontrol – through the partial reduction of isothiocyanates with the in situ generated Schwartz reagent. The high electrophilicity of the starting materials enables the straightforward addition of the hydride ion, thus constituting a reliable and high-yielding method for obtaining variously functionalized thioformamides. Sensitive chemical groups to the reduction conditions such as nitro, ester, alkene, azo, azide and keto groups do not interfere with the chemoselectivity of the process. Moreover, the stereochemical information embodied in the starting material is fully retained in the final products. The synthetic potential of the selected thioformamide template is also briefly discussed.

A hemithioindigo molecular motor for metal surface attachment by Kerstin Hoffmann; Peter Mayer; Henry Dube (1979-1983).
Functionalization of surfaces with responsive molecular entities is currently an important research field allowing the organization of molecular functions in space in a defined way and thus accessing emergent properties not observed in solution. Herein we report on the synthesis of a hemithioindigo molecular motor bearing thioether feet for surface attachment on its thioindigo fragment. We also give a full theoretical description of its ground state energy profile together with an experimental evaluation of the visible light driven unidirectional rotation in solution. Comparison with the corresponding unsubstituted original motor shows that after feet-attachment the hemithioindigo molecular motor is fully operative with a similar maximum attainable speed and degree of unidirectionality.

Self-assembled micro-fibres by oxime connection of linear peptide amphiphiles by Richard Booth; Ignacio Insua; Ghibom Bhak; Javier Montenegro (1984-1991).
Linear peptide amphiphiles are excellent biocompatible scaffolds for the hierarchical self-assembly of one-dimensional nano-structures in aqueous media. However, their structural exploration and screening of self-assembling properties are often limited by time-consuming synthesis and purification steps. We here describe the application of an oxime bond as a powerful synthetic tool towards the conjugation of peptide heads bearing a hydroxylamine group with hydrophobic aldehyde tails. This methodology allowed the quick preparation of a small library of oxime-connected peptide amphiphiles, whose supramolecular screening revealed nano-to-micro-fibrillation with dependency on their chemical structure. These results demonstrate the simplicity and the synthetic potential of the oxime conjugation for the preparation of peptide amphiphiles with improved self-assembling capabilities.

Investigations into the DNA-binding mode of doxorubicinone by Samuel Steucek Tartakoff; Jennifer M. Finan; Ellis J. Curtis; Haley M. Anchukaitis; Danielle J. Couture; Samantha Glazier (1992-1998).
Cancer treatment is one of the major challenges facing the modern biomedical profession. Development of new small-molecule chemotherapeutics requires an understanding of the mechanism of action for these treatments, as well as the structure–activity relationship. Study of the well-known DNA-intercalating agent, doxorubicin, and its aglycone, doxorubicinone, was undertaken using a variety of spectroscopic and calorimetric techniques. It was found that, despite conservation of the planar, aromatic portion of doxorubicin, the agylcone does not intercalate; it instead likely binds to the DNA minor-groove.

Protic additives or impurities promote imine reduction with pinacolborane by Blake S. N. Huchenski; Alexander W. H. Speed (1999-2004).
We report here that addition of stoichiometric amounts of alcohols or water to mixtures of imines and pinacolborane promote reduction reactions. The reactions of several imines were examined, revealing that alkyl imines were reduced, while aniline derived imines were not effectively reduced. The use of binol as an additive resulted in modest enantioinduction, however other chiral additives that were screened gave negligible enantioinduction. While the reactions described herein are not competitive in conversion with established imine reduction technologies, this work reveals that the presence of protic impurities must be considered as a promoter of side reactions in catalyzed imine hydroborations. Amines also promote imine reduction in certain cases, raising the possibility of a slow autocatalytic reaction. The ability of water or other protic impurities to promote the reduction of imines with pinacolborane represents an important identification of a potential source of background reaction in catalyzed reductions of imines.

One-pot stapling of interchain disulfides of antibodies using an isobutylene motif by Shuang Sun; Padma Akkapeddi; Marta C. Marques; Nuria Martínez-Sáez; Vukosava M. Torres; Carlos Cordeiro; Omar Boutureira; Gonçalo J. L. Bernardes (2005-2012).
Monoclonal antibodies have emerged as an important class of therapeutics in oncological and autoimmune diseases due to their several attractive properties, such as high binding affinity and specificity. However, it has recently become clear that antibodies recovered from serum show a significantly decreased potency owing to various reasons, including deamidation, oxidation, fragment antigen binding (Fab) exchange, and disulfide shuffling. Fab exchange and disulfide shuffling result because of the instability of disulfides in serum. Herein, we reported a ‘one-pot’ stapling strategy using isobutylene motifs to stabilise the interchain disulfides of antibodies. This general method was applied to a Fab fragment of the anti-HER2 antibody. The stapled Fab was completely stable in the presence of biological thiols. The approach was further applied to two different full-length IgGs, trastuzumab and rituximab, under mild and biocompatible conditions. The binding affinity of the antibody was enhanced, relative to its native form, after being stapled. The stapled structure maintained its effector functions and behaved similarly to its native form in vivo. This work provides a straightforward and scalable method for the stabilisation of antibodies in various formats.

An atom- and step-economical C(sp3)–H addition of N,N-dimethyl anilines to various sterically demanding 1,1- and 1,2-disubstituted alkenes has been achieved by using a simple β-diketiminato ligand supported scandium dialkyl complex in combination with a borate compound. The corresponding C(sp3)–C(sp3) bond forming reaction occurs with excellent regioselectivities to give a variety of tertiary aromatic amines.

Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor by Steven E. Kirberger; Peter D. Ycas; Jorden A. Johnson; Chen Chen; Michael F. Ciccone; Rinette W. L. Woo; Andrew K. Urick; Huda Zahid; Ke Shi; Hideki Aihara; Sean D. McAllister; Mohammed Kashani-Sabet; Junwei Shi; Alex Dickson; Camila O. dos Santos; William C. K. Pomerantz (2020-2027).
Bromodomain and PHD finger containing protein transcription factor (BPTF) is an epigenetic protein involved in chromatin remodelling and is a potential anticancer target. The BPTF bromodomain has one reported small molecule inhibitor (AU1, rac-1). Here, advances made on the structure–activity relationship of a BPTF bromodomain ligand are reported using a combination of experimental and molecular dynamics simulations leading to the active enatiomer (S)-1. Additionally, a ligand deconstruction analysis was conducted to characterize important pharmacophores for engaging the BPTF bromodomain. These studies have been enabled by a protein-based fluorine NMR approach, highlighting the versatility of the method for selectivity, ligand deconstruction, and ligand binding. To enable future analysis of biological activity, cell growth analyses in a panel of cancer cell lines were carried out using CRISPR-Cas9 and (S)-1 to identify cell-based model systems that are sensitive to BPTF inhibition.

Correction for ‘An elusive thermal [2 + 2] cycloaddition driven by visible light photocatalysis: tapping into strain to access C2-symmetric tricyclic rings’ by Kamaljeet Singh et al., Org. Biomol. Chem., 2018, DOI: 10.1039/c8ob01273c.

Back cover (2029-2030).