High-throughput catch-and-release synthesis of oxazoline hydroxamates. Structure-activity relationships in novel inhibitors of Escherichia coli LpxC: in vitro enzyme inhibition and antibacterial properties

Novel Hydroxamic Acids Containing Aryl-Substituted 1,2,4- or 1,3,4-Oxadiazole Backbones and an Investigation of Their Antibiotic Potentiation Activity

UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a zinc amidase that catalyzes the second step of the biosynthesis of lipid A, which is an outer membrane essential structural component of Gram-negative bacteria. Inhibitors of this enzyme can be attributed to two main categories, non-hydroxamate and hydroxamate inhibitors, with the latter being the most effective given the chelation of Zn2+ in the active site. Compounds containing diacetylene or acetylene tails and the sulfonic head, as well as oxazoline derivatives of hydroxamic acids, are among the LpxC inhibitors with the most profound antibacterial activity. The present article describes the synthesis of novel functional derivatives of hydroxamic acids-bioisosteric to oxazoline inhibitors-containing 1,2,4- and 1,3,4-oxadiazole cores and studies of their cytotoxicity, antibacterial activity, and antibiotic potentiation. Some of the hydroxamic acids we obtained (9c, 9d, 23a, 23c, 30b, 36) showed significant potentiation in nalidixic acid, rifampicin, and kanamycin against the growth of laboratory-strain Escherichia coli MG1655. Two lead compounds (9c, 9d) significantly reduced Pseudomonas aeruginosa ATCC 27853 growth in the presence of nalidixic acid and rifampicin.

Catalytic Amide Activation with Thermally Stable Molybdenum(VI) Dioxide Complexes

Oxazolines and thiazolines are important constituents of bioactive natural products and pharmaceuticals. Here, we report the development of an effective and practical method of oxazoline and thiazoline formation, which can facilitate the synthesis of natural products, chiral ligands, and pharmaceutical intermediates. This method capitalized on a Mo(VI) dioxide catalyst stabilized by substituted picolinic acid ligands, which is tolerant to many functional groups that would otherwise be sensitive to highly electrophilic alternative reagents.

Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives

Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.

Substituent-Controlled Regioselective Photoinduced Cyclization of N-Allylbenzamides with N-Sulfonylaminopyridinium Salts

The annulation reactions of N-allylbenzamides with N-sulfonylaminopyridinium salts were developed under metal-free photoinduced mild conditions. Substituent-controlled sulfonaminoarylation and sulfonaminooxylation of benzamides were realized: N-allylbenzamides lead to benzosultams, while N-(2-phenylallyl)benzamides give sulfonamidylated oxazoline derivatives. Control experiments indicated that those reactions undergo a radical pathway with arylsulfonamidyl radicals as the intermediates. The aryl C-H bond functionalization in arylsulfonamidyl was involved for the first time to give benzosultams.

A Facile Synthesis of 2-Oxazolines via Dehydrative Cyclization Promoted by Triflic Acid

2-oxazolines are common moieties in numerous natural products, pharmaceuticals, and functional copolymers. Current methods for synthesizing 2-oxazolines mainly rely on stoichiometric dehydration agents or catalytic dehydration promoted by specific catalysts. These conditions either generate stoichiometric amounts of waste or require forcing azeotropic reflux conditions. As such, a practical and robust method that promotes dehydrative cyclization while generating no byproducts would be attractive to oxazoline production. Herein, we report a triflic acid (TfOH)-promoted dehydrative cyclization of N-(2-hydroxyethyl)amides for synthesizing 2-oxazolines. This reaction tolerates various functional groups and generates water as the only byproduct. This method affords oxazoline with inversion of α-hydroxyl stereochemistry, suggesting that alcohol is activated as a leaving group under these conditions. Furthermore, the one-pot synthesis protocol of 2-oxazolines directly from carboxylic acids and amino alcohols is also provided.

Electrochemical oxidative cyclization of N-allylcarboxamides: efficient synthesis of halogenated oxazolines

Herein, we reported an efficient and sustainable intramolecular electrochemical cyclization of N-allylcarboxamides for the synthesis of various halogenated oxazolines.

One-pot access to 2-oxazolines via a Castro-Stephens coupling and intramolecular cyclization

Aim:

Here, we have reported easy one-pot access to a series of oxazolines using a modified Castro-Stephens coupling protocol.

Background:

2-oxazolines have been shown to have significant biological activity and wide-ranging applications in organic chemistry. These properties make oxazolines as heterocyclic compounds of immense importance.

Objective:

The objective of this study is to synthesize oxazoline derivatives via an economical and one-pot protocol.

Method:

2-oxazoline has been synthesized through Cu-powder mediated Castro-Stephens coupling and intramolecular cyclization route. The mechanism involves a rearrangement in which one of the oxygen from the N-acylamino alcohol group is liberated as water and then transferred to alkyne functionality to form 2-oxazoline derivatives. The oxazolines were characterized by NMR, mass, and XRD studies.

Result:

The protocol is economically viable and uses readily available Cu-powder along with DMF for cross-coupling and cyclization steps.

Rearrangement of 3-Hydroxyazetidines into 2-Oxazolines

A novel rearrangement sequence of 3-hydroxyazetidines via a Ritter initiated cascade provides highly substituted 2-oxazolines in high yields. The reaction conditions and substrate scope of the transformation have been studied demonstrating the generality of the process. The derived products can also be functionalized in order to undergo further intramolecular cyclization leading to a new class of macrocycle. The final cyclization step was shown to be a transformation amenable to continuous flow processing allowing for a dramatic reduction in the reaction time and simple scale-up.

Targeting Metalloenzymes for Therapeutic Intervention

Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.

Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae

The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn⁺² dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K. pneumoniae LpxC (KpLpxC) topology distinct from its orthologous counterparts in other bacterial species. Molecular docking study of the protein recognized receptor antagonist compound 106, a uridine-based LpxC inhibitory compound, as a ligand best able to fit the binding pocket with a Gold Score of 67.53. Molecular dynamics simulation of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. The ligand tail exhibited preferred binding to the domain I residues as opposed to the substrate binding hydrophobic channel of subdomain II, usually targeted by inhibitory compounds. Comparison with the undocked KpLpxC system demonstrated ligand induced high conformational changes in the hydrophobic channel of subdomain II in KpLpxC. Hence, ligand exerted its inhibitory potential by rendering the channel unstable for substrate binding.

Electrosynthesis of Trisubstituted 2-Oxazolines via Dehydrogenative Cyclization of β-Amino Arylketones

An electrochemically intramolecular functionalization of C(sp³)-H bonds with masked oxygen nucleophiles was developed. With KI as the catalyst and electrolyte, diverse trisubstituted 2-oxazolines were constructed in good to excellent yields. This newly developed electrochemical dehydrogenative approach features external oxidant-free and additive-free conditions.

Efficient Synthesis of Substituted 2-(4H-1,3-benzoxazin-2-yl)Phenols via a Pseudo Three-Component Reaction

An efficient pseudo three-component reaction between substituted 2-hydroxybenzaldehydes and ammonium acetate for the preparation of substituted 2-(4 H-1,3-benzoxazin-2-yl)phenols in moderate to good yields (70-80%) was developed. The structure of a typical product was confirmed by X-ray crystallography.

A 'photorelease, catch and photorelease' strategy for bioconjugation utilizing a p-hydroxyphenacyl group

A bioorthogonal 'catch and photorelease' strategy, which combines alkyne-azide cycloaddition between p-hydroxyphenacyl azide and alkyne derivatives to form a 1,2,3-triazole adduct and subsequent photochemical release of the triazole moiety via a photo-Favorskii rearrangement, is introduced. The first step can also involve photorelease of a strained alkyne and its Cu-free click reaction with azide.

Multicomponent reactions: a sustainable tool to 1,2- and 1,3-azoles

The present review outlines the recent advancements and pioneering efforts on the synthesis of 1,2/1,3-azoles employing a multicomponent strategy.

Synthesis of benzo[1,3]oxazines via copper(i)-catalyzed cascade annulation of nitriles, aldehydes and diaryliodonium salts

A copper(i)-catalyzed one-pot [2 + 2 + 2] cascade annulation reaction of diaryliodoniums, nitriles, and aldehydes has been developed for the efficient synthesis of 2,4-substituted benzoxazine derivatives.

Visible-light-mediated radical oxydifluoromethylation of olefinic amides for the synthesis of CF2H-containing heterocycles

The visible-light-mediated oxydifluoromethylation of olefinic amides with difluoromethyl sulfones has been explored.

Visible-light-induced photocatalytic oxytrifluoromethylation of N-allylamides for the synthesis of CF3-containing oxazolines and benzoxazines

A visible-light-induced photocatalytic oxytrifluoromethylation reaction of N-allylamides has been developed for the efficient synthesis of CF3-containing oxazolines and benzoxazines under mild reaction conditions.

Lipid A as a Drug Target and Therapeutic Molecule

In this review, lipid A, from its discovery to recent findings, is presented as a drug target and therapeutic molecule. First, the biosynthetic pathway for lipid A, the Raetz pathway, serves as a good drug target for antibiotic development. Several assay methods used to screen for inhibitors of lipid A synthesis will be presented, and some of the promising lead compounds will be described. Second, utilization of lipid A biosynthetic pathways by various bacterial species can generate modified lipid A molecules with therapeutic value.

Copper-triggered three-component reaction of CF3CHN2, nitriles, and aldehydes: highly diastereoselective synthesis of CF3-substituted oxazolines and vicinal amino alcohols

A novel, catalytic, three-component C–C, C–N and C–O bond forming reaction to afford CF₃-substituted oxazolines is realized.

Divergent Regioselectivity in Photoredox-Catalyzed Hydrofunctionalization Reactions of Unsaturated Amides and Thioamides

A direct method to construct 2-oxazolines and 2-thiazolines from corresponding allylic amides and thioamides is reported. The redox-neutral intramolecular hydrofunctionalization is enabled by a dual catalyst system comprised of the 9-mesityl-N-methyl acridinium tetrafluoroborate and phenyl disulphide and exhibits complete selectivity for the anti-Markovnikov regioisomeric products. The cyclization of allylic thioamides is postulated to operate via a modified mechanism in which oxidation of the thioamide, rather than the alkene, is responsible for the observed reactivity.

Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer

The emergence of antibiotic-resistant strains of pathogenic bacteria is an increasing threat to global health that underscores an urgent need for an expanded antibacterial armamentarium. Gram-negative bacteria, such as Escherichia coli, have become increasingly important clinical pathogens with limited treatment options. This is due in part to their lipopolysaccharide (LPS) outer membrane components, which dually serve as endotoxins while also protecting Gram-negative bacteria from antibiotic entry. The LpxC enzyme catalyzes the committed step of LPS biosynthesis, making LpxC a promising target for new antibacterials. Here, we present the first structure of an LpxC enzyme in complex with the deacetylation reaction product, UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine. These studies provide valuable insight into recognition of substrates and products by LpxC and a platform for structure-guided drug discovery of broad spectrum Gram-negative antibiotics.

Structure based design of an in vivo active hydroxamic acid inhibitor of P. aeruginosa LpxC

Lipid A is an essential component of the Gram negative outer membrane, which protects the bacterium from attack of many antibiotics. The Lipid A biosynthesis pathway is essential for Gram negative bacterial growth and is unique to these bacteria. The first committed step in Lipid A biosynthesis is catalysis by LpxC, a zinc dependent deacetylase. We show the design of an LpxC inhibitor utilizing a robust model which directed efficient design of picomolar inhibitors. Analysis of physiochemical properties drove design to focus on an optimal lipophilicity profile. Further structure based design took advantage of a conserved water network over the active site, and with the optimal lipophilicity profile, led to an improved LpxC inhibitor with in vivo activity against wild type Pseudomonas aeruginosa.

4D-LQTA-QSAR and docking study on potent Gram-negative specific LpxC inhibitors: a comparison to CoMFA modeling

A quasi 4D-QSAR has been carried out on a series of potent Gram-negative LpxC inhibitors. This approach makes use of the molecular dynamics (MD) trajectories and topology information retrieved from the GROMACS package. This new methodology is based on the generation of a conformational ensemble profile, CEP, for each compound instead of only one conformation, followed by the calculation intermolecular interaction energies at each grid point considering probes and all aligned conformations resulting from MD simulations. These interaction energies are independent variables employed in a QSAR analysis. The comparison of the proposed methodology to comparative molecular field analysis (CoMFA) formalism was performed. This methodology explores jointly the main features of CoMFA and 4D-QSAR models. Step-wise multiple linear regression was used for the selection of the most informative variables. After variable selection, multiple linear regression (MLR) and partial least squares (PLS) methods used for building the regression models. Leave-N-out cross-validation (LNO), and Y-randomization were performed in order to confirm the robustness of the model in addition to analysis of the independent test set. Best models provided the following statistics: [Formula in text] (PLS) and [Formula in text] (MLR). Docking study was applied to investigate the major interactions in protein-ligand complex with CDOCKER algorithm. Visualization of the descriptors of the best model helps us to interpret the model from the chemical point of view, supporting the applicability of this new approach in rational drug design.

Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold

Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors based on a diphenyl-diacetylene (1,4-diphenyl-1,3-butadiyne) threonyl-hydroxamate scaffold. These studies provide a molecular interpretation for the differential antibiotic activities of compounds with a substituted distal phenyl ring as well as the absolute stereochemical requirement at the C2, but not C3, position of the threonyl group.

Fluorescence-based methods to assay inhibitors of lipopolysaccharide synthesis

Treatment of infections caused by Gram-negative bacteria is difficult due in large part to problems arising from innate and acquired drug resistance, resulting in a limited number of effective antibiotics. Consequently, antibiotics that can circumvent mechanisms of drug resistance are needed. Lipid A is a glucosamine phospholipid that acts as an anchor for lipopolysaccharides (LPS) that comprise the outer membranes of Gram-negative bacteria, a barrier for small molecule entry into the cell, and is also the portion of LPS that stimulates the immune system in septic shock. Consequently, inhibitors of lipid A biosynthesis have the potential to function as antibiotics and/or anti-endotoxins in the treatment of Gram-negative bacterial infections. Current efforts in the development of antibiotics targeted against lipid A have focused on the metal-dependent deacetylase LpxC. Herein we describe fluorescence-based assays that can be used for the evaluation of LpxC inhibitors with the potential to serve as antibiotics.

Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design

LpxC is an essential enzyme in the lipid A biosynthetic pathway in gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different gram-negative pathogens. We report that inhibitors with a diacetylene scaffold effectively overcome the resistance caused by sequence variation in the LpxC substrate-binding passage. Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale. These observations highlight the need for a molecular understanding of inherent structural features and conformational plasticity of LpxC enzymes for optimizing LpxC inhibitors as broad-spectrum antibiotics against gram-negative infections.

QSAR models to predict mutagenicity of acrylates, methacrylates and alpha,beta-unsaturated carbonyl compounds

OBJECTIVE

The purpose of this study is to develop a quantitative structure-activity relationship (QSAR) model that can distinguish mutagenic from non-mutagenic species with alpha,beta-unsaturated carbonyl moiety using two endpoints for this activity - Ames test and mammalian cell gene mutation test - and also to gather information about the molecular features that most contribute to eliminate the mutagenic effects of these chemicals.

METHODS

Two data sets were used for modeling the two mutagenicity endpoints: (1) Ames test and (2) mammalian cells mutagenesis. The first one comprised 220 molecules, while the second one 48 substances, ranging from acrylates, methacrylates to alpha,beta-unsaturated carbonyl compounds. The QSAR models were developed by applying linear discriminant analysis (LDA) along with different sets of descriptors computed using the DRAGON software.

RESULTS

For both endpoints, there was a concordance of 89% in the prediction and 97% confidentiality by combining the three models for the Ames test mutagenicity. We have also identified several structural alerts to assist the design of new monomers.

SIGNIFICANCE

These individual models and especially their combination are attractive from the point of view of molecular modeling and could be used for the prediction and design of new monomers that do not pose a human health risk.

A new class of UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) inhibitors for the treatment of Gram-negative infections: PCT application WO 2008027466

BACKGROUND

Human infections due to Gram-negative bacteria cause significant morbidity and mortality. Identification of new strategies, molecular targets, and agents for the treatment of Gram-negative bacterial infections are needed urgently. Lipid A is a necessary component of the lipopolysaccharide-containing outer membrane of Gram-negative bacteria. The zinc-dependent hydrolase UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) involved in the first committed step in the biosynthetic pathway of lipid A has no sequence homology to any known mammalian enzymes and has emerged as an attractive Gram-negative antibacterial molecular target. Most previously described LpxC inhibitors contain a hydroxamic acid, which can lead to low specificity vs. other metal-dependent enzymes and can consequently result in unwanted side effects.

OBJECTIVE

This review examines a new reported class of nonhydroxamic LpxC inhibitors for the treatment of Gram-negative infections.

METHODS

The new class of inhibitor is compared with several previously reported LpxC inhibitors.

CONCLUSION

The LpxC inhibitors disclosed in PCT application WO 2008027466 contain hydantoins in place of the hydroxamic acids commonly found in most previously described inhibitors. These molecules could represent a means of treating Gram-negative infections via a more selective inhibition of LpxC.