Catalytic Staudinger—Vilarrasa Reaction for the Direct Ligation of Carboxylic Acids and Azides

Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity

In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.

Single-Component Electroactive Polymer Architectures for Non-Enzymatic Glucose Sensing

Organic mixed ionic-electronic conductors (OMIECs) have emerged as promising materials for biological sensing, owing to their electrochemical activity, stability in an aqueous environment, and biocompatibility. Yet, OMIEC-based sensors rely predominantly on the use of composite matrices to enable stimuli-responsive functionality, which can exhibit issues with intercomponent interfacing. In this study, an approach is presented for non-enzymatic glucose detection by harnessing a newly synthesized functionalized monomer, EDOT-PBA. This monomer integrates electrically conducting and receptor moieties within a single organic component, obviating the need for complex composite preparation. By engineering the conditions for electrodeposition, two distinct polymer film architectures are developed: pristine PEDOT-PBA and molecularly imprinted PEDOT-PBA. Both architectures demonstrated proficient glucose binding and signal transduction capabilities. Notably, the molecularly imprinted polymer (MIP) architecture demonstrated faster stabilization upon glucose uptake while it also enabled a lower limit of detection, lower standard deviation, and a broader linear range in the sensor output signal compared to its non-imprinted counterpart. This material design not only provides a robust and efficient platform for glucose detection but also offers a blueprint for developing selective sensors for a diverse array of target molecules, by tuning the receptor units correspondingly.

Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications

Protein biosynthesis is a central process in all living cells that is catalyzed by a complex molecular machine─the ribosome. This process is termed translation because the language of nucleotides in mRNAs is translated into the language of amino acids in proteins. Transfer RNA (tRNA) molecules charged with amino acids serve as adaptors and recognize codons of mRNA in the decoding center while simultaneously the individual amino acids are assembled into a peptide chain in the peptidyl transferase center (PTC). As the nascent peptide emerges from the ribosome, it is threaded through a long tunnel referred to as a nascent peptide exit tunnel (NPET). The PTC and NPET are the sites targeted by many antibiotics and are thus of tremendous importance from a biomedical perspective and for drug development in the pharmaceutical industry.Researchers have achieved much progress in characterizing ribosomal translation at the molecular level; an impressive number of high-resolution structures of different functional and inhibited states of the ribosome are now available. These structures have significantly contributed to our understanding of how the ribosome interacts with its key substrates, namely, mRNA, tRNAs, and translation factors. In contrast, much less is known about the mechanisms of how small molecules, especially antibiotics, affect ribosomal protein synthesis. This mainly concerns the structural basis of small molecule-NPET interference with cotranslational protein folding and the regulation of protein synthesis. Growing biochemical evidence suggests that NPET plays an active role in the regulation of protein synthesis.Much-needed progress in this field is hampered by the fact that during the preparation of ribosome complexes for structural studies (i.e., X-ray crystallography, cryoelectron microscopy, and NMR spectroscopy) the aminoacyl- or peptidyl-tRNAs are unstable and become hydrolyzed. A solution to this problem is the application of hydrolysis-resistant mimics of aminoacyl- or peptidyl-tRNAs.In this Account, we present an overview of synthetic methods for the generation of peptidyl-tRNA analogs. Modular approaches have been developed that combine (i) RNA and peptide solid-phase synthesis on 3'-aminoacylamino-adenosine resins, (ii) native chemical ligations and Staudinger ligations, (iii) tailoring of tRNAs by the selective cleavage of natural native tRNAs with DNAzymes followed by reassembly with enzymatic ligation to synthetic peptidyl-RNA fragments, and (iv) enzymatic tailing and cysteine charging of the tRNA to obtain modified CCA termini of a tRNA that are chemically ligated to the peptide moiety of interest. With this arsenal of tools, in principle, any desired sequence of a stably linked peptidyl-tRNA mimic is accessible. To underline the significance of the synthetic conjugates, we briefly point to the most critical applications that have shed new light on the molecular mechanisms underlying the context-specific activity of ribosome-targeting antibiotics, ribosome-dependent incorporation of multiple consecutive proline residues, the incorporation of d-amino acids, and tRNA mischarging.Furthermore, we discuss new types of stably charged tRNA analogs, relying on triazole- and squarate (instead of amide)-linked conjugates. Those have pushed forward our mechanistic understanding of nonribosomal peptide synthesis, where aminoacyl-tRNA-dependent enzymes are critically involved in various cellular processes in primary and secondary metabolism and in bacterial cell wall synthesis.

Iron-Catalyzed Synthesis of α-Azido α-Amino Esters via the Alkylazidation of Alkenes

An iron-catalyzed alkylazidation of dehydroamino acids using peroxides as alkyl radical precursors is described. Non-natural azidated amino esters bearing an α-alkyl chain could be obtained in 18-94% yields using TMSN3 as an azide source. The obtained α-alkyl-α-azide α-amino esters could be further functionalized through cycloaddition or azide reduction with amide couplings to afford aminal-type peptides, α-triazolo amino acids, and tetrahydro-triazolopyridine, showing the great versatility of this now easily accessible class of amino acids.

Influence of protecting groups on O- and C-glycosylation with neuraminyl and ulosonyl dibutylphosphates

The adamantanyl thioglycosides of 5-isothiocyano and 5-azido 5-desamino-4,7,8,9-tetra-O-acetylneuraminic acid methyl ester were converted into the corresponding dibutyl phosphates, which proved to be excellent α-selective donors for O-sialidation with a range of typical acceptors, and good donors for reaction with allyltributylstannane, albeit without significant anomeric selectivity. In the KDN series the dibuylphosphate derived from a donor carrying a 4,5-cyclic carbonate protecting group afforded the corresponding C-glycoside with excellent α-selectivity on activation in the presence of allyltributylstannane, whereas the corresponding donor carrying acetate esters at the 4- and 5-positions was unselective. Overall, it is revealed that while the strongly electron-withdrawing isothiocyanato and azido groups are sufficient to promote highly α-selective O-sialidation, they are inadequate when faced with less reactive nucleophiles when mixtures of anomers are obtained.

Metal-Free C-N or C-C Bond Cleavages of α-Azido Ketones: An Oxidative-Amidation Strategy for the Synthesis of α-Ketothioamides and Amides

A novel metal-free oxidative-amidation strategy for the synthesis of α-ketothioamides and amides from α-azido ketones was developed. The C-H bond thionation of α-azido ketones with elemental sulfur could form α-ketothioacyl azide, which was then nucleophilically attacked by amines, causing the cleavage of the C-N bond to afford α-ketothioamides, while amides could be formed with the release of nitrogen gas and cyano anion in the presence of PhI(OAc)₂ by selective C-C bond cleavage.

A metal-free approach for the synthesis of amides/esters with pyridinium salts of phenacyl bromides via oxidative C-C bond cleavage

An efficient, simple, and metal-free synthetic approach for the N- and O-benzoylation of various amines/benzyl alcohols with pyridinium salts of phenacyl bromides is demonstrated to generate the corresponding amides and esters. This protocol facilitates the oxidative cleavage of a C–C bond followed by formation of a new C–N/C–O bond in the presence of K₂CO₃. Various pyridinium salts of phenacyl bromides can be readily transformed into a variety of amides and esters which is an alternative method for the conventional amidation and esterification in organic synthesis. High functional group tolerance, broad substrate scope and operational simplicity are the prominent advantages of the current protocol.

An efficient and practical synthesis of formylglycinamide ribonucleotide (FGAR)

An efficient five-step synthetic route for multigram-scale preparation of formylglycinamide ribonucleotide (FGAR) from peracetylated β-d-ribofuranosyl azide has been developed.

The implementation of the catalytic Staudinger–Vilarrasa reaction in polymer chemistry as a highly efficient chemistry strategy

A versatile and highly efficient chemistry strategy, the catalytic S–V reaction of acids with azides, was firstly implemented in polymer chemistry for the construction of various amide-containing polymers.

Hemilability-Driven Water Activation: A NiII Catalyst for Base-Free Hydration of Nitriles to Amides

The Ni^II complex 1 containing pyridyl- and hydroxy-functionalized N-heterocyclic carbenes (NHCs) is synthesized and its catalytic utility for the selective nitrile hydration to the corresponding amide under base-free conditions is evaluated. The title compound exploits a hemilabile pyridyl unit to interact with a catalytically relevant water molecule through hydrogen-bonding and promotes a nucleophilic water attack to the nitrile. A wide variety of nitriles is hydrated to the corresponding amides including the pharmaceutical drugs rufinamide, Rifater, and piracetam. Synthetically challenging α-hydroxyamides are accessed from cyanohydrins under neutral conditions. Related catalysts that lack the pyridyl unit (i.e., compounds 2 and 4) are not active whereas those containing both the pyridyl and the hydroxy or only the pyridyl pendant (i.e., compounds 1 and 3) show substantial activity. The linkage isomer 1' where the hydroxy group is bound to the metal instead of the pyridyl group was isolated under different crystallization conditions insinuating a ligand hemilabile behavior. Additional pK_a measurements reveal an accessible pyridyl unit under the catalytic conditions. Kinetic studies support a ligand-promoted nucleophilic water addition to a metal-bound nitrile group. This work reports a Ni-based catalyst that exhibits functional hemilability for hydration chemistry.

Nonclassical Routes for Amide Bond Formation

The present review offers an overview of nonclassical (e.g., with no pre- or in situ activation of a carboxylic acid partner) approaches for the construction of amide bonds. The review aims to comprehensively discuss relevant work, which was mainly done in the field in the last 20 years. Organization of the data follows a subdivision according to substrate classes: catalytic direct formation of amides from carboxylic and amines ( section 2 ); the use of carboxylic acid surrogates ( section 3 ); and the use of amine surrogates ( section 4 ). The ligation strategies (NCL, Staudinger, KAHA, KATs, etc.) that could involve both carboxylic acid and amine surrogates are treated separately in section 5 .

A telescopic one-pot synthesis of β-lactam rings using amines as a convenient source of imines

A facile synthetic approach to substituted β-lactams was designed, using secondary benzylic amines and acid chlorides as starting materials. The reactions proceeded smoothly and all the products were obtained in good yields.

Carboxyl activation via silylthioesterification: one-pot, two-step amidation of carboxylic acids catalyzed by non-metal ammonium salts

The first organo-catalyzed silylthioesterification of a carboxylic acid and a commercially available mercaptoorganosilane results in the in situ production of an O-silylthionoester. Subsequent amine addition forms amides in an operationally simple one-pot procedure without removal of water. The scope and efficiency of these reactions with respect to the catalyst, carboxylic acid, amine, [Si─S] moiety, and solvent are investigated. A number of functionalities are tolerated in the two-step amidation including alkene, alkyne, alkyl and aryl halides, benzylic ethers, and heterocycles with free coordinating sites.

Ante versus post-functionalization to control surface structures with superhydrophobic and superoleophobic properties

Here, we report the first use of the Staudinger–Vilarrasa reaction with perfluorinated surface modification.

Design of glycosyltransferase inhibitors targeting human O-GlcNAc transferase (OGT)

Inhibition of glycosyltransferases requires the design of neutral inhibitors to allow cell permeation as mimicks of their natural dianionic substrates.

Selective Radical Amination of Aldehydic C(sp2)-H Bonds with Fluoroaryl Azides via Co(II)-Based Metalloradical Catalysis: Synthesis of N-Fluoroaryl Amides from Aldehydes under Neutral and Nonoxidative Conditions

The Co(II) complex of the D_2h-symmetric amidoporphyrin 3,5-Di ^t Bu-IbuPhyrin, [Co(P1)], has proven to be an effective metalloradical catalyst for intermolecular amination of C(sp²)-H bonds of aldehydes with fluoroaryl azides. The [Co(P1)]-catalyzed process can employ aldehydes as the limiting reagents and operate under neutral and non-oxidative conditions, generating nitrogen gas as the only byproduct. The metalloradical aldehydic C-H amination is suitable for different combinations of aldehydes and fluoroaryl azides, producing the corresponding N-fluoroaryl amides in good to excellent yields. A series of mechanistic studies support a stepwise radical mechanism for the Co(II)-catalyzed intermolecular C-H amination.

Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate

A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger-Vilarrasa amide-bond formation, and azide-alkyne click chemistry. The compounds were evaluated as inhibitors of five metal-dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn(2+) ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)-Gal substrate with little interaction with the enzyme.

Staudinger ligation as a method for bioconjugation

In 1919 the German chemist Hermann Staudinger was the first to describe the reaction between an azide and a phosphine. It was not until recently, however, that Bertozzi and co-workers recognized the potential of this reaction as a method for bioconjugation and transformed it into the so-called Staudinger ligation. The bio-orthogonal character of both the azide and the phosphine functions has resulted in the Staudinger ligation finding numerous applications in various complex biological systems. For example, the Staudinger ligation has been utilized to label glycans, lipids, DNA, and proteins. Moreover, the Staudinger ligation has been used as a synthetic method to construct glycopeptides, microarrays, and functional biopolymers. In the emerging field of bio-orthogonal ligation strategies, the Staudinger ligation has set a high standard to which most of the new techniques are often compared. This Review summarizes recent developments and new applications of the Staudinger ligation.

Synthesis of amidomethyltrifluoroborates and their use in cross-coupling reactions

Amidomethyltrifluoroborates were successfully synthesized in a one-pot fashion and used in cross-coupling reactions with a wide variety of aryl and heteroaryl chlorides.

An improved route to PUGNAc and its galacto-configured congener

An efficient, scalable, and reliable synthesis of PUGNAc and its galacto-configured congener is reported.