Identification of the lydiamycin biosynthetic gene cluster in a plant pathogen guides structural revision and identification of molecular target

The natural products actinonin and matlystatin feature an N-hydroxy-2-pentyl-succinamyl (HPS) chemophore that facilitates metal chelation and confers their metalloproteinase inhibitory activity. Actinonin is the most potent natural inhibitor of peptide deformylase (PDF) and exerts antimicrobial and herbicidal bioactivity by disrupting protein synthesis. Here, we used a genomics-led approach to identify candidate biosynthetic gene clusters (BGCs) hypothesized to produce HPS-containing natural products. We show that one of these BGCs is on the pathogenicity megaplasmid of the plant pathogen Rhodococcus fascians and produces lydiamycin A, a macrocyclic pentapeptide. The presence of genes predicted to make an HPS-like chemophore informed the structural recharacterization of lydiamycin via NMR and crystallography to show that it features a rare 2-pentyl-succinyl chemophore. We demonstrate that lydiamycin A inhibits bacterial PDF in vitro and show that a cluster-situated PDF gene confers resistance to lydiamycin A, representing an uncommon self-immunity mechanism associated with the production of a PDF inhibitor. In planta competition assays showed that lydiamycin enhances the fitness of R. fascians during plant colonization. This study highlights how a BGC can inform the structure, biochemical target, and ecological function of a natural product.

Development and Applications of an Amide Linchpin Reagent

Linchpin reagents are building blocks that can be chemoselectively functionalized to afford products with a common, useful functional group. In this work, we describe the development and validation of the first amide linchpin reagent and demonstrate its use as a doubly electrophilic building block for the synthesis of a variety of amides, including challenging classes. The linchpin reagent was first functionalized via rhodium-catalyzed electrophilic amination. Selected masked C-isocyanate products were then further derivatized with Grignard reagents to produce secondary amides, or tertiary amides if an alkylating agent was added subsequently. The success of this sequence relies on fully controlled reactivity at each electrophilic site, first exploiting the weak N-O bond and then, the ability to form the free isocyanate intermediate in situ. The overall transformation proceeds with high chemoselectivity, demonstrating the ability of this new linchpin reagent to form amides through atypical bond construction. Finally, the potential of this reagent as a more broadly applicable NCO linchpin is demonstrated by the formation of lactams and unsymmetrical ureas.

Innovations in isocyanate synthesis for a sustainable future

Isocyanates play a crucial role as key building blocks in the production of thermoplastic foams, elastomers, adhesives, agrochemicals, and pharmaceuticals. These compounds are essential in the manufacture of various polymeric products, such as polyurethane foams, synthetic rubbers, and surface coatings. Given their significance, and the fact that many isocyanates are highly reactive and toxic, there is an increasing demand for innovative and sustainable methods for their synthesis and detection that emphasize safety, efficiency, and selectivity. Developing processes for isocyanate production that avoid hazardous reagents like phosgene is particularly critical. While several methods exist for the in situ generation of isocyanates, the search for an eco-friendly and sustainable approach for their direct synthesis and isolation continues. Recent advances in isocyanate synthesis promise innovative and efficient strategies with broad industrial and environmental benefits. This review highlights various methods for synthesizing di- and monoisocyanates, emphasizing their isolation and conversion into ureas and carbamates in line with the principles of sustainable and green chemistry.

Stereoretentive Decarboxylative Amidation of α,β-Unsaturated Carboxylic Acids to Access Enamides

Enamides have emerged as robust alternatives for enamines, exhibiting versatile reactivity for further synthetic modifications, including nucleophilic addition, cycloaddition, and asymmetric hydrogenation. While transition-metal-catalyzed cross-coupling of alkenyl (pseudo)halides with amides has been widely employed to construct this valuable scaffold, it suffers from some limitations, such as the need for transition-metal catalysts and the preparative synthesis of alkenyl (pseudo)halides. In this study, we report a mild and convenient stereoretentive decarboxylative amidation of α,β-unsaturated carboxylic acids with easily procurable 1,4,2-dioxazol-5-ones, providing a practical synthetic route to enamides. Density functional theory (DFT) calculations revealed a plausible reaction mechanism, which involves the nucleophilic addition of a carboxylate onto dioxazolone, followed by sequential concerted rearrangements.

Electron Donor-Acceptor Complex-Assisted Photochemical Conversion of O-2-Nitrobenzyl Protected Hydroxamates to Amides

The hydroxamic acid functionality is present in various medicinal agents and has attracted special interest for synthetic transformations in both organic and medicinal chemistry. The N-O bond cleavage of hydroxamic acid derivatives provides an interesting transformation for the generation of various products. We demonstrate, herein, that O-benzyl-type protected hydroxamic acids may undergo photochemical N-O bond cleavage, in the presence or absence of a catalyst, leading to amides. Although some O-benzyl protected aromatic hydroxamates may be photochemically converted to amides in the presence of a base and anthracene as the catalyst, employing O-2-nitrobenzyl group allowed the smooth conversion of both aliphatic and aromatic hydroxamates to primary or secondary amides in good to excellent yields in the presence of an amine, bypassing the need of a catalyst. DFT and UV-Vis studies supported the effective generation of an electron donor-acceptor (EDA) complex between O-2-nitrobenzyl hydroxamates and amines, which enabled the successful product formation under these photochemical conditions. An extensive substrate scope was demonstrated, showcasing that both aliphatic and aromatic hydroxamates are compatible with this protocol, affording a wide variety of primary and secondary amides.

Slow-Binding and Covalent HDAC Inhibition: A New Paradigm?

The dysregulated post-translational modification of proteins is an established hallmark of human disease. Through Zn2+-dependent hydrolysis of acyl-lysine modifications, histone deacetylases (HDACs) are key regulators of disease-implicated signaling pathways and tractable drug targets in the clinic. Early targeting of this family of 11 enzymes (HDAC1-11) afforded a first generation of broadly acting inhibitors with medicinal applications in oncology, specifically in cutaneous and peripheral T-cell lymphomas and in multiple myeloma. However, first-generation HDAC inhibitors are often associated with weak-to-modest patient benefits, dose-limited efficacies, pharmacokinetic liabilities, and recurring clinical toxicities. Alternative inhibitor design to target single enzymes and avoid toxic Zn2+-binding moieties have not overcome these limitations. Instead, recent literature has seen a shift toward noncanonical mechanistic approaches focused on slow-binding and covalent inhibition. Such compounds hold the potential of improving the pharmacokinetic and pharmacodynamic profiles of HDAC inhibitors through the extension of the drug-target residence time. This perspective aims to capture this emerging paradigm and discuss its potential to improve the preclinical/clinical outlook of HDAC inhibitors in the coming years.

Photo-cycloaddition reactions of vinyldiazo compounds

Heterocyclic rings are important structural scaffolds encountered in both natural and synthetic compounds, and their biological activity often depends on these motifs. They are predominantly accessible via cycloaddition reactions, realized by either thermal, photochemical, or catalytic means. Various starting materials are utilized for this purpose, and, among them, diazo compounds are often encountered, especially vinyldiazo compounds that give access to donor-acceptor cyclopropenes which engage in [2+n] cycloaddition reactions. Herein, we describe the development of photochemical processes that produce diverse heterocyclic scaffolds from multisubstituted oximidovinyldiazo compounds. High chemoselectivity, good functional group tolerance, and excellent scalability characterize this methodology, thus predisposing it for broader applications. Experimental and computational studies reveal that under light irradiation these diazo reagents selectively transform into cyclopropenes which engage in cycloaddition reactions with various dipoles, while under thermal conditions the formation of pyrazole from vinyldiazo compounds is favored.

From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Discovery of YSR734: A Covalent HDAC Inhibitor with Cellular Activity in Acute Myeloid Leukemia and Duchenne Muscular Dystrophy

Histone deacetylases (HDACs) have emerged as powerful epigenetic modifiers of histone/non-histone proteins via catalyzing the deacetylation of ε-N-acetyl lysines. The dysregulated activity of these Zn2+-dependent hydrolases has been broadly implicated in disease, notably cancer. Clinically, the recurring dose-limiting toxicities of first-generation HDACi sparked a paradigm shift toward safer isoform-specific molecules. With pervasive roles in aggressive diseases, there remains a need for novel approaches to target these enzymes. Herein, we report the discovery of YSR734, a first-in-class covalent HDACi, with a 2-aminobenzanilide Zn2+ chelate and a pentafluorobenzenesulfonamide electrophile. This class I selective proof of concept modified HDAC2Cys274 (catalytic domain), with nM potency against HDAC1-3, sub-μM activity in MV4-11 cells, and limited cytotoxicity in MRC-9 fibroblasts. In C2C12 myoblasts, YSR734 activated muscle-specific biomarkers myogenin/Cav3, causing potent differentiation into myotubes (applications in Duchenne Muscular Dystrophy). Current efforts are focused on improving in vivo ADME toward a preclinical covalent HDACi.

A critical assessment on stability behaviour of Vorinostat using LC-MS-QTOF with H/D exchange and NMR

Vorinostat is the first USFDA-approved HDAC inhibitor for the treatment of cutaneous t-cell lymphoma. Vorinostat was exposed to ICH-recommended hydrolytic (acid, base, and neutral), oxidative, thermal, and photolytic stress conditions to understand the degradation behaviour. A Stability indicating LC method was developed and validated for separating and identifying forced degradation products. Under different stress conditions, six degradants were identified and characterized by LC-HRMS, MS/MS, and hydrogen-deuterium exchange mass studies. Vorinostat was found to be highly susceptible to the acidic and basic environment. In contrast, the drug substance was stable in the solid state under thermal and photolytic conditions whereas, it was found moderately stable when photolytic stress was provided to dissolved state of Vorinostat in acetonitrile-water. The degradants were identified as 7-amino-N-phenylheptanamide, 8-hydrazineyl-8-oxo-N-phenyloctanamide, 8-oxo-8-(phenylamino)octanoic acid, 8-oxo-8-(2-(7-oxo-7-(phenylamino)heptyl)hydrazineyl)-N-phenyloctanamide, 8,8'-(1-hydroxyhydrazine-1,2-diyl)bis(8-oxo-N-phenyloctanamide), and N1-((8-oxo-8-(phenylamino)octanoyl)oxy)-N8-phenyloctanediamide. The mechanistic explanation for the formation of each degradant in stability conditions has also been derived. The major degradants were also isolated/synthesized and characterized through 1H NMR for preparing impurity standards. Additionally, in-silico toxicity of the degradants was predicted in comparison to the drug, to identify whether any degradant has any specific type of toxicity and requires special focus to set specification limits during formulation development. The predicted toxicity indicated that the degradants have similar safety profile as that of the drug and specification can be set as per general impurity guideline.

Condition-Controlled O-Acylation and N-O Bond Reduction of Hydroximic Acids with Thioacetic Acid

Condition-dependent transformations between hydroximic acids and thioacetic acid were achieved. Using NH₄HCO₃ in the ethanol solvent, efficient N-O bond cleavage of hydroxamic acids occurred to afford primary amides with high functional group compatibility. The reaction was switched to O-acylation when NEt₃ and H₂O were used as the base and solvent, respectively. These facile transformations could be scaled up to the gram level smoothly. Preliminary mechanistic studies suggested that the N-O bond cleavage involves a cascade process of acylation/reduction.

Synthesis of Nε-acetyl-L-homolysine by the Lossen rearrangement and its application for probing deacetylases and binding modules of acetyl-lysine

Lysine acetylation is a posttranslational protein modification mediating protein-protein interactions by recruitment of bromodomains. Investigations of bromodomains have focused so far on the sequence context of the modification site and acyl-modifications installed at lysine side chains. In contrast, there is only little information about the impact of the lysine residue that carries the modification on bromodomain binding. Here, we report a synthesis strategy for L-acetyl-homolysine from L-2-aminosuberic acid by the Lossen rearrangement. Peptide probes containing acetylated homolysine, lysine, and ornithine were generated and used for probing the binding preferences of four bromodomains from three different families. Tested bromodomains showed distinct binding patterns, and one of them bound acetylated homolysine with similar efficiency as the native substrate containing acetyl-lysine. Deacetylation assays with a bacterial sirtuin showed a strong preference for acetylated lysine, despite a broad specificity for N-acyl modifications.

Incorporation of Rhodamine into a Host Polymer via In-Situ Generated Isocyanato Group and Application for the Detection of Cu2+ Ion

A rhodamine-based fluorescent polymer P(MMA-co-RB) has been synthesized via an intermediate NCO-containing polymer generated by the Lossen rearrangement reaction. The fluorescent property of P(MMA-co-RB) with regard to metal ions, such as Cu2+, Fe3+, Cr3+, Al3+, Zn2+, Co2+, Sn2+ and Ag+, was studied by fluorescence emission spectroscopy. The results demonstrate that the fluorescence intensity of P(MMA-co-RB) decreased gradually with an increase of the concentration of Cu2+ ion. Furthermore, a test strip made of P(MMA-co-RB) can be used for fast and quantitative determination of Cu2+ ion. In the presence of Cu2+ ion, the sensory tester undergoes distinct changes in fluorescence intensity and visible color.

Photoinduced Transition-Metal-Free Chan-Evans-Lam-Type Coupling: Dual Photoexcitation Mode with Halide Anion Effect

Herein, we report a photoinduced transition-metal-free C(aryl)-N bond formation between 2,4,6-tri(aryl)boroxines or arylboronic acids as an aryl source and 1,4,2-dioxazol-5-ones (dioxazolones) as an amide coupling partner. Chloride anion, either generated in situ by photodissociation of chlorinated solvent molecules or added separately as an additive, was found to play a critical cooperative role, thereby giving convenient access to a wide range of synthetically versatile N-arylamides under mild photo conditions. The synthetic virtue of this transition-metal-free Chan-Evans-Lam-type coupling was demonstrated by large-scale reactions, synthesis of 15N-labeled arylamides, and applicability toward biologically relevant compounds. On the basis of mechanistic investigations, two distinctive photoexcitations are proposed to function in the current process, in which the first excitation involving chloro-boron adduct facilitates the transition-metal-free activation of dioxazolones by single electron transfer (SET), and the second one enables the otherwise-inoperative 1,2-aryl migration of the thus-formed N-chloroamido-borate adduct.

Organic Isocyanates and Isothiocyanates: Versatile Intermediates in Agrochemistry

In recent decades, organic isocyanates and isothiocyanates have been often applied as reactive intermediates in research syntheses or manufacturing routes of many agrochemicals. These heterocumulenes allowed the installation of crucial carboxylic functions, such as carbamates, ureas, and semicarbazones, but have also been used for the construction of five- and six-membered heterocycles, such as tetrazolones, thiazoles, and uracils.

1 Introduction

2 Preparation of Carboxylic Acid Functions

3 Preparation of Heterocyclic Rings

4 Conclusion

CHNO isomers and derivatives – a computational overview

A state-of-the-art computational study of CHNO isomers is presented, including substituted derivatives and cyclotrimerization and deprotonation products.

Interrupted Curtius Rearrangements of Quaternary Proline Derivatives: A Flow Route to Acyclic Ketones and Unsaturated Pyrrolidines

Conversion of N-Boc-protected quaternary proline derivatives under thermal Curtius rearrangement conditions was found to afford a series of ring-opened ketone and unsaturated pyrrolidine products instead of the expected carbamate species. The nature of the substituent on the quaternary carbon thereby governs the product outcome due to the stability of a postulated N-acyliminium species. A continuous flow process with in-line scavenging was furthermore developed to streamline this transformation and safely create products on a gram scale.

Chemical Upcycling of Waste Poly(bisphenol A carbonate) to 1,4,2-Dioxazol-5-ones and One-Pot C-H Amidation

Chemical upcycling of poly(bisphenol A carbonate) (PC) was achieved in this study with hydroxamic acid nucleophiles, giving rise to synthetically valuable 1,4,2-dioxazol-5-ones and bisphenol A. Using 1,5,7-triazabicyclo[4.4.0]-dec-5-ene (TBD), non-green carbodiimidazole or phosgene carbonylation agents used in conventional dioxazolone synthesis were successfully replaced with PC, and environmentally harmful bisphenol A was simultaneously recovered. Assorted hydroxamic acids exhibited good-to-excellent efficiencies and green chemical features, promising broad synthetic application scope. In addition, a green aryl amide synthesis process was developed, involving one-pot depolymerization from polycarbonate to dioxazolone followed by rhodium-catalyzed C-H amidation, including gram-scale examples with used compact discs.

Inhibitors of histone deacetylase 6 based on a novel 3-hydroxy-isoxazole zinc binding group

Histone deacetylase 6 (HDAC6) is an established drug target for cancer treatment. Inhibitors of HDAC6 based on a hydroxamic acid zinc binding group (ZBG) are often associated with undesirable side effects. Herein, we describe the identification of HDAC6 inhibitors based on a completely new 3-hydroxy-isoxazole ZBG. A series of derivatives decorated with different aromatic or heteroaromatic linkers, and various cap groups were synthesised and biologically tested. In vitro tests demonstrated that some compounds are able to inhibit HDAC6 with good potency, the best candidate reaching an IC₅₀ of 700 nM. Such good potency obtained with a completely new ZBG make these compounds particularly attractive. The effect of the most active inhibitors on the acetylation levels of histone H3 and α- tubulin and their anti-proliferative activity of DU145 cells were also investigated. Docking studies were performed to evaluate the binding mode of these new derivatives and discuss structure-activity relationships.

Hydroxamic Acid Derivatives: From Synthetic Strategies to Medicinal Chemistry Applications

Since the approval of three hydroxamic acid-based HDAC inhibitors as anticancer drugs, such functional groups acquired even more notoriety in synthetic medicinal chemistry. The ability of hydroxamic acids (HAs) to chelate metal ions makes this moiety an attractive metal binding group-in particular, Fe(III) and Zn(II)-so that HA derivatives find wide applications as metalloenzymes inhibitors. In this minireview, we will discuss the most relevant features concerning hydroxamic acid derivatives. In a first instance, the physicochemical characteristics of HAs will be summarized; then, an exhaustive description of the most relevant methods for the introduction of such moiety into organic substrates and an overview of their uses in medicinal chemistry will be presented.

Mechanochemical Rearrangements

Molecular rearrangements are a powerful tool for constructing complex structures in an atom- and step-economic manner, translating multistep transformations into an intrinsically more sustainable process. Mechanochemical molecular rearrangements become an even more appealing eco-friendly synthetic approach, especially for preparing active pharmaceutical ingredients (APIs) and natural products. Still in their infancy, rearrangements promoted by mechanochemistry represent a promising approach for chemists to merge molecular diversity and green chemistry perspectives toward more selective and efficient syntheses with a reduced environmental footprint.

Electrochemical rearrangement protocols towards the construction of diverse molecular frameworks

Rearrangement reactions constitute a critical facet of synthetic organic chemistry and demonstrate an attractive way to take advantage of existing structures to access various important molecular frameworks. Electroorganic chemistry has emerged as an environmentally benign approach to carry out organic transformations by directly employing an electric current and avoids the use of stoichiometric chemical oxidants. The last few years have witnessed a resurgence of electroorganic chemistry that has promoted a renaissance of interest in the development of novel redox electroorganic transformations. This review manifests the evolution of electrosynthesis in the area of rearrangement chemistry and covers the achievements in the field of migration, ring expansion, and rearrangements along with the mechanisms involved.

N,N-Diacylaminals as Emerging Tools in Synthesis: From Peptidomimetics to Asymmetric Catalysis

N,N-Diacylaminals are flexible molecular scaffolds that have commonly been utilized as amide surrogates in peptidomimetics. The singularities of this motif as an N-acyl imine equivalent and as hydrogen-bond donor have recently opened new synthetic opportunities, especially in the field of asymmetric catalysis. This concept article highlights this diverse synthetic potential and provides the elements necessary for further developments.

Lifetimes of the Aglycone Substrates of Specifier Proteins, the Autonomous Iron Enzymes That Dictate the Products of the Glucosinolate-Myrosinase Defense System in Brassica Plants

Specifier proteins (SPs) are components of the glucosinolate-myrosinase defense system found in plants of the order Brassicales (brassicas). Glucosinolates (GLSs) comprise at least 150 known S-(β-d-glucopyranosyl)thiohydroximate-O-sulfonate compounds, each with a distinguishing side chain linked to the central carbon. Following tissue injury, the enzyme myrosinase (MYR) promiscuously hydrolyzes the common thioglycosidic linkage of GLSs to produce unstable aglycone intermediates, which can readily undergo a Lossen-like rearrangement to the corresponding organoisothiocyanates. The known SPs share a common protein architecture but redirect the breakdown of aglycones to different stable products: epithionitrile (ESP), nitrile (NSP), or thiocyanate (TFP). The different effects of these products on brassica consumers motivate efforts to understand the defense response in chemical detail. Experimental analysis of SP mechanisms is challenged by the instability of the aglycones and would be facilitated by knowledge of their lifetimes. We developed a spectrophotometric method that we used to monitor the rearrangement reactions of the MYR-generated aglycones from nine GLSs, discovering that their half-lives (t_1/2) vary by a factor of more than 50, from <3 to 150 s (22 °C). The t_1/2 of the sinigrin-derived allyl aglycone (34 s), which can form the epithionitrile product (1-cyano-2,3-epithiopropane) in the presence of ESP, proved to be sufficient to enable spatial and temporal separation of the MYR and ESP reactions. The results confirm recent proposals that ESP is an autonomous iron-dependent enzyme that intercepts the unstable aglycone rather than a direct effector of MYR. Knowledge of aglycone lifetimes will enable elucidation of how the various SPs reroute aglycones to different products.