Amide Hydrolysis Research Articles

Pyrazinamide drug resistance in RpsA mutant (∆438A) of Mycobacterium tuberculosis: Dynamics of essential motions and free-energy landscape analysis.

Pyrazinamide is an essential first-line antitubercular drug which plays pivotal role in tuberculosis treatment. It is a prodrug that requires amide hydrolysis by mycobacterial pyrazinamidase enzyme for conversion into pyrazinoic acid (POA). POA is known to target ribosomal protein S1 (RpsA), aspartate decarboxylase (PanD), and some other mycobacterial proteins. Spontaneous chromosomal mutations in RpsA have been reported for phenotypic resistance against pyrazinamide. We have constructed and validated 3D models of the native and Δ438A mutant form of RpsA protein. RpsA protein variants were then docked to POA and long range molecular dynamics simulations were carried out. Per residue binding free-energy calculations, free-energy landscape analysis, and essential dynamics analysis were performed to outline the mechanism underlying the high-level PZA resistance conferred by the most frequently occurring deletion mutant of RpsA. Our study revealed the conformational modulation of POA binding site due to the disruptive collective modes of motions and increased conformational flexibility in the mutant than the native form. Residue wise MMPBSA decomposition and protein-drug interaction pattern revealed the difference of energetically favorable binding site in the wild-type (WT) protein in comparison with the mutant. Analysis of size and shape of minimal energy landscape area delineated higher stability of the WT complex than the mutant form. Our study provides mechanistic insights into pyrazinamide resistance in Δ438A RpsA mutant, and the results arising out of this study will pave way for design of novel and effective inhibitors targeting the resistant strains of Mycobacterium tuberculosis.

Correlations between metabolism and structural elements of the alicyclic fentanyl analogs cyclopropyl fentanyl, cyclobutyl fentanyl, cyclopentyl fentanyl, cyclohexyl fentanyl and 2,2,3,3-tetramethylcyclopropyl fentanyl studied by human hepatocytes and LC-QTOF-MS

Recently, a number of fentanyl analogs have been implicated in overdose deaths in Europe and in the US. So far, little is known of the molecular behavior of the structurally related subgroup; the alicyclic fentanyls. In this study, reference standards of cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and 2,2,3,3-tetramethylcyclopropyl fentanyl (TMCPF) at a final concentration of 5 µM were incubated with cryopreserved human hepatocytes (1 × 106 cells/mL) for 0, 1, 3 and 5 h. The metabolites formed were identified by liquid chromatography–quadrupole time-of-flight mass spectrometry analysis. The most abundant biotransformation found was N-dealkylation (formation of normetabolites) and oxidation of the alicyclic rings. As ring size increased, the significance of N-dealkylation decreased in favor of alicyclic ring oxidation. An example of this was cyclopropyl fentanyl, with a three-carbon ring, whose normetabolite covered 82% of the total metabolic peak area and no oxidation of the alicyclic ring was observed. In contrast, TMCPF, with a seven-carbon ring structure, rendered as much as 85% of its metabolites oxidized on the alicyclic ring. Other biotransformations found included oxidation of the piperidine ethyl moiety and/or the phenethyl substructure, glucuronidation as well as amide hydrolysis to form metabolites identical to despropionyl fentanyl. Taken together, this study provides a base for understanding the metabolism of a number of structurally related fentanyl analogs formed upon intake.

FAAH-Catalyzed C-C Bond Cleavage of a New Multitarget Analgesic Drug.

The discovery of extended catalytic versatilities is of great importance in both the chemistry and biotechnology fields. Fatty acid amide hydrolase (FAAH) belongs to the amidase signature superfamily and is a major endocannabinoid inactivating enzyme using an atypical catalytic mechanism involving hydrolysis of amide and occasionally ester bonds. FAAH inhibitors are efficacious in experimental models of neuropathic pain, inflammation, and anxiety, among others. We report a new multitarget drug, AGN220653, containing a carboxyamide-4-oxazole moiety and endowed with efficacious analgesic and anti-inflammatory activities, which are partly due to its capability of achieving inhibition of FAAH, and subsequently increasing the tissue concentrations of the endocannabinoid anandamide. This inhibitor behaves as a noncompetitive, slowly reversible inhibitor. Autoradiography of purified FAAH incubated with AGN220653, opportunely radiolabeled, indicated covalent binding followed by fragmentation of the molecule. Molecular docking suggested a possible nucleophilic attack by FAAH-Ser241 on the carbonyl group of the carboxyamide-4-oxazole moiety, resulting in the cleavage of the C-C bond between the oxazole and the carboxyamide moieties, instead of either of the two available amide bonds. MRM-MS analyses only detected the Ser241-assisted formation of the carbamate intermediate, thus confirming the cleavage of the aforementioned C-C bond. Quantum mechanics calculations were fully consistent with this mechanism. The study exemplifies how FAAH structural features and mechanism of action may override the binding and reactivity propensities of substrates. This unpredicted mechanism could pave the way to the future development of a completely new class of amidase inhibitors, of potential use against pain, inflammation, and mood disorders.

Unexpected Resistance to Base-Catalyzed Hydrolysis of Nitrogen Pyramidal Amides Based on the 7-Azabicyclic[2.2.1]heptane Scaffold.

Non-planar amides are usually transitional structures, that are involved in amide bond rotation and inversion of the nitrogen atom, but some ground-minimum non-planar amides have been reported. Non-planar amides are generally sensitive to water or other nucleophiles, so that the amide bond is readily cleaved. In this article, we examine the reactivity profile of the base-catalyzed hydrolysis of 7-azabicyclo[2.2.1]heptane amides, which show pyramidalization of the amide nitrogen atom, and we compare the kinetics of the base-catalyzed hydrolysis of the benzamides of 7-azabicyclo[2.2.1]heptane and related monocyclic compounds. Unexpectedly, non-planar amides based on the 7-azabicyclo[2.2.1]heptane scaffold were found to be resistant to base-catalyzed hydrolysis. The calculated Gibbs free energies were consistent with this experimental finding. The contribution of thermal corrections (entropy term, –TΔS‡) was large; the entropy term (ΔS‡) took a large negative value, indicating significant order in the transition structure, which includes solvating water molecules.

Hydroaminocarbonylation of Alkynes to Produce Primary α,β‐Unsaturated Amides Using NH4HCO3 Dually as Ammonia Surrogate and Brønsted Acid Additive

AbstractBy using NH4HCO3 dually as ammonia surrogate and Brønsted acid additive, the production of primary α,β‐unsaturated amides via hydroaminocarbonylation of alkynes was accomplished efficiently. The advantages of using the solid and inexpensive NH4HCO3 included: (1) the facile and clean manipulation without presence of stinky gaseous NH3 or liquids organic amines, (2) the inhibition of the subsequent dehydration and hydrolysis of amides due to its weak basicity, and (3) the facilitated formation of Pd−H catalytic active species by the released H2CO3 serving as a weak Brønsted acid additive. In addition, the diphopshine of Dppp with the natural bite angle (βn) of 91° was found indispensable to spur the performance of the palladium catalyst for this reaction. Both terminal and internal phenylacetylene derivatives could be used as the substrates, affording the corresponding primary α,β‐unsaturated amides in good yields along with excellent regio‐selectivities to the branched ones.

Artificial Zinc Enzymes with Fine-Tuned Active Sites for Highly Selective Hydrolysis of Activated Esters

Zinc enzymes are ubiquitous in nature and are frequently used to catalyze the hydrolysis of carboxylic acid esters, phosphate esters, and amides. Although many models and mimics of zinc enzymes have been reported, it remains difficult to construct active sites with accurately positioned catalytic groups and tunable substrate selectivity. By imprinting a substrate-like amino template coordinated to a polymerizable zinc complex inside cross-linked micelles, we prepared water-soluble nanoparticles with well-defined active sites. The position of the zinc ion could be tuned systematically with respect to the ester bond to be cleaved in the substrate (p-nitrophenyl esters), as well as the rigidity of the active site. Our imprinted zinc catalysts were able to distinguish substrates that differed by the position of a single methyl group, chain length of the acyl chain, and substitution of the phenyl ring. The turnover number (>460 at pH 7) was 1 order of magnitude higher than those previously reported for artific...

LC-ESI-MS/MS identification and characterization of ponatinib in vivo phase I and phase II metabolites

Ponatinib (Iclusig®) is a multi-targeted tyrosine kinase inhibitor (TKIs). It is active against T315I and other BCR-ABL mutants. Investigation of in vivo metabolism of ponatinib was done using Sprague Dawley rats by giving one oral dose of PNT (4.7 mg/kg) to each rat and urine samples were gathered at several time intervals from dosing. Filteration of urine samples was done through 0.45 μm syringe filters. Phase separation using ACN was applied for extraction of ponatinib related metabolites. Characterization and identification of one in vivo phase II metabolite and thirteen in vivo phase I of PNT were done using LC-MS/MS. Phase I metabolic reactions were reduction, N-demethylation, hydroxylation, N-oxidation, oxidation and amide hydrolysis. Phase II metabolic reaction was glucuronidation of hydroxyl benzyl metabolites of ponatinib. The major in vivo metabolic reactions were α hydroxylation and α oxidation at piperazine ring. Literature review revealed no articles that have been published on in vivo metabolism of ponatinib in Sprague Dawley rats or ponatinib in vivo phase I and phase II metabolites structural characterization and identification.

Scaffold-Hopping Approach To Discover Potent, Selective, and Efficacious Inhibitors of NF-κB Inducing Kinase.

NF-κB-inducing kinase (NIK) is a protein kinase central to the noncanonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which has been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism. We report herein the discovery of lead chemical series of NIK inhibitors that were identified through a scaffold-hopping strategy using structure-based design. Electronic and steric properties of lead compounds were modified to address glutathione conjugation and amide hydrolysis. These highly potent compounds exhibited selective inhibition of LTβR-dependent p52 translocation and transcription of NF-κB2 related genes. Compound 4f is shown to have a favorable pharmacokinetic profile across species and to inhibit BAFF-induced B cell survival in vitro and reduce splenic marginal zone B cells in vivo.

On the hydrolysis mechanisms of amides and peptides

AbstractHere the possibility is raised that peptide hydrolysis, in the absence of catalysis by proteases or buffers, may still have a self‐catalyzing mechanism that differs from ordinary amide hydrolysis. Second, an attempt is made to clarify the ongoing confusion in the computational chemistry literature regarding the rate‐limiting step in ordinary amide hydrolysis. Third, Gibbs activation energies (free‐energy barriers) for formamide hydrolysis are derived from rate constants and presented under different concentration conventions, for ease of comparison to values from computational chemistry predictions past and future.

Sensitive quantification of 5F-NNEI and characterization of its several metabolites in authentic urine and/or serum specimens obtained from three individuals by LC–QTRAP-MS/MS and high-resolution LC–Orbitrap-MS/MS

A synthetic cannabinoid 5F-NNEI and its metabolites in authentic human specimens have not been reported yet. The aim of this study is, firstly, to establish a sensitive quantification method of 5F-NNEI in human serum and urine specimens, and, secondly, the characterization of its metabolites in authentic urine specimens obtained from three individuals. These compounds were extracted from β-glucuronide-hydrolyzed and unhydrolyzed urine and/or serum specimens via liquid-liquid extraction. The identification and quantification were performed using liquid chromatography (LC)–QTRAP tandem mass spectrometry (MS/MS), and the characterization of the metabolites was done using LC–high-resolution-MS/MS. The limits of detection for unchanged 5F-NNEI were 6 pg/mL with the quantification range of 10–2000 pg/mL in serum, and 3 pg/mL with the quantification range of 5–1000 pg/mL in urine. The devised method was applied to quantify 5F-NNEI in authentic serum and/or urine specimens from three individuals. The levels of 5F-NNEI were 11.6 and 3680 pg/mL in serum specimens of cases 1 and 2, respectively, and were 5.07 and 7.90 pg/mL in urine specimens of cases 2 and 3, respectively. Several metabolites of 5F-NNEI produced by amide hydrolysis, defluorination, hydroxylation, carboxylation and/or glucuronization were tentatively identified in the urine specimens by the LC–high-resolution-MS/MS. A synthetic cannabinoid, 5F-NNEI, was identified and quantified in its unchanged form, and its several metabolites were tentatively identified in authentic specimens obtained from three individuals, for the first time to our knowledge.

Spiro Bicyclic Guanidino Compounds from Pufferfish: Possible Biosynthetic Intermediates of Tetrodotoxin in Marine Environments.

Tetrodotoxin (TTX, 1) is a potent neurotoxin that is widely found in both terrestrial and marine animals; however, the biosynthetic pathway and genes for TTX have not yet been elucidated. Previously, we proposed that TTX originated from a monoterpene; this hypothesis was based on the structures of cyclic guanidino compounds that are commonly found in toxic newts. However, these compounds have not been detected in marine organisms. Instead, a series of deoxy analogues of TTX were found in toxic marine animals; thus, we further screened for TTX-related compounds in marine animals. Herein, we report seven novel spiro bicyclic guanidino compounds 2-8 that were isolated from the pufferfish Tetraodon biocellatus. In compounds 2-5 and 7-8, a six-membered cyclic guanidino amide is spiro-fused with 2,4-dimethyl cyclohexane, whereas in compound 6, the same cyclic guanidino amide is spiro-fused with 2,3,5-trimethylcyclopentane. Compounds 2-5 and 7-8 have the same carbon skeleton and relative configuration as TTX. Thus, we proposed that compounds 2-8 are biosynthetic intermediates of TTX in marine environments. TTX could be biosynthetically derived from compound 7 via intermediates 2-5 through several oxidations, amide hydrolysis, and formation of the hemiaminal and lactone found in 5,6,11-trideoxyTTX, the major TTX analogue, whereas compounds 6 and 8 might be shunt products. LC-MS analysis confirmed the wide distribution of compounds 2, 3, or both in TTX-containing marine animals, namely pufferfish, crab, octopus, and flatworm, but compounds 2-8 were not detected in newts.

The opposite effect of K+ and Na+ on the hydrolysis of linear and cyclic dipeptides

Potassium and sodium are generally considered inert ‘spectator’ ions for organic reactions. Here, we report rate constants for the acid-promoted hydrolysis of the seven dipeptides of glycine (G) and alanine (A) and an unexpected pattern in how these rates differ in the presence of K+ and Na+. The linear dipeptides hydrolyze 12–18% percent slower in the presence of KCl versus an equal concentration of NaCl, while the cyclic dipeptides hydrolyze 5–13% faster in the presence of KCl (all P-values < 0.025). We believe this is the first report of a general organic reaction—here, amide hydrolysis—for which some substrates react faster in the presence of K+ and others in Na+. The results offer a potential reason for life’s mysterious universal selection of intracellular potassium over sodium.

Modular Synthesis of β-Amino Boronate Peptidomimetics

Herein, we describe the synthesis of novel β-amino boronate peptidomimetics from amphoteric α-borylaldehydes in the Ugi multicomponent reaction. A mild deprotection method provided the free and stable boronic acid forms of the target molecules, which display notable stability toward protodeborylation. Despite the presence of Lewis acidic boron, there is no evidence for hydrolysis of the adjacent amide via a 5- or 6-membered ring intermediate. This methodology should facilitate the development of libraries of new boron-containing antibiotics and antifungal agents.

Tumor‐Specific Self‐Degradable Nanogels as Potential Carriers for Systemic Delivery of Anticancer Proteins

AbstractDevelopment of a safe and effective carrier for systemic protein delivery is highly desirable, which depends on management of the relationship among loading capacity, stability, delivery efficiency, and degradability. Here, a tumor‐specific self‐degradable nanogel composed of hyaluronidase (HAase)‐degradable hyaluronic acid (HA) matrices entrapping acid‐activatable HAase (aHAase) for systemic delivery of anticancer proteins is reported. Collaboratively crosslinked nanogels (cNG) obtained by the synthetic cholesteryl methacrylated HA show high protein‐loading capacity and stability. The aHAase is engineered by modifying the HAase with citraconic anhydride to shield its HA‐degrading activity, which can be reversibly activated by hydrolysis of the citraconic amide under acidic condition. In the tumor microenvironment, the mild acidity activates the aHAase partially, which results in swelling of the cNG and releasing of the aHAase. The released reactivated aHAase can degrade the HA that is also a major constituent of tumor extracellular matrix to increase perfusion of the cNG in the tumor stroma. In the acidic endocytic vesicles, the aHAase is fully reactivated. The active aHAase completely degrades the cNG to release the encapsulated anticancer protein, deoxyribonuclease I intracellularly, which digests the DNA to cause tumor cell death for enhanced antitumor efficacy.

Metabolic Hydrolysis of Aromatic Amides in Selected Rat, Minipig, and Human In Vitro Systems

The release of aromatic amines from drugs and other xenobiotics resulting from the hydrolysis of metabolically labile amide bonds presents a safety risk through several mechanisms, including geno-, hepato- and nephrotoxicity. Whilst multiple in vitro systems used for studying metabolic stability display serine hydrolase activity, responsible for the hydrolysis of amide bonds, they vary in their efficiency and selectivity. Using a range of amide-containing probe compounds (0.5–10 µM), we have investigated the hydrolytic activity of several rat, minipig and human-derived in vitro systems - including Supersomes, microsomes, S9 fractions and hepatocytes - with respect to their previously observed human in vivo metabolism. In our hands, human carboxylesterase Supersomes and rat S9 fractions systems showed relatively poor prediction of human in vivo metabolism. Rat S9 fractions, which are commonly utilised in the Ames test to assess mutagenicity, may be limited in the detection of genotoxic metabolites from aromatic amides due to their poor concordance with human in vivo amide hydrolysis. In this study, human liver microsomes and minipig subcellular fractions provided more representative models of human in vivo hydrolytic metabolism of the aromatic amide compounds tested.

SYNTHESIS OF DESGLYMIDODRINE FROM MIDODRINE BY CONVENTIONAL AMIDE HYDROLYSIS METHOD

Objective: The term prodrug involves chemically modifying inert compound which upon administration releases the active parent drug to elicit its pharmacological response within the body. Acting as a α-adrenergic agonist, desglymidodrine an active metabolite of amide prodrug midodrine is used for the treatment of essential and orthostatic hypotension. In the present study synthesis of desglymidodrine from midodrine was reported.Methods: The synthesis was done by the conventional amide hydrolysis method.Results: A novel synthesis of desglymidodrine was successfully achieved and spectrally elucidated by infrared spectroscopy (IR), 1H, 13C nuclear magnetic resonance (NMR) and mass analysis.Conclusion: The acquired results were found to be accurate, the synthetic route appeared to be simple, cost-effective and time efficient. Hence the synthesized desglymidodrine can be as a reference standard for the estimation of the same.

Water proton NMR detection of amide hydrolysis and diglycine dimerization.

The transverse relaxation rate of water protons R2(1H2O) is found to be sensitive to amide hydrolysis and diglycine dimerization. The results demonstrate the feasibility of using R2(1H2O) as a diagnostic tool to detect chemical changes in aqueous solutions. Potential applications include drug product formulation and inspection.

Development of a flow injection analytical system for short chain amide determination based on a tubular bioreactor and an ammonium sensor.

Pseudomonas aeruginosa (P. aeruginosa) possesses intracellular amidase activity, which catalyses the hydrolysis of short aliphatic amides producing NH4+, and has already been used along with an ammonium ion selective electrode for amide quantification. However, the incorporation of a biological membrane turned to be a challenging process and either the final arrangement was prone to amidase losses or the recovery of the sensor coating after the interaction took too long. In this article a flow injection system with an ammonium acoustic wave sensor is proposed, and after testing several different arrangements for the biological element, the ultimate choice consisted of the immobilization of a P. aeruginosa cell-free extract in the inner wall of a tubular glass reactor, which resulted in a reliable analytical system. Response times less than one minute and complete recovery in less than two minutes assured conveniently fast analysis. The analytical system, as long as the column was properly stored in HEPES buffer containing 2 mM β-mercaptoethanol and 1 mM benzamidine and refrigerated when not in use, could be used at least for 20 working days, along a period of one month, maintaining the initial sensitivity.

PH-responsive charge-reversal polymer-functionalized boron nitride nanospheres for intracellular doxorubicin delivery.

BackgroundAnticancer drug-delivery systems (DDSs) capable of responding to the physiological stimuli and efficiently releasing drugs inside tumor cells are highly desirable for effective cancer therapy. Herein, pH-responsive, charge-reversal poly(allylamine hydrochlorid)−citraconic anhydride (PAH-cit) functionalized boron nitride nanospheres (BNNS) were fabricated and used as a carrier for the delivery and controlled release of doxorubicin (DOX) into cancer cells.MethodsBNNS was synthesized through a chemical vapor deposition method and then functionalized with synthesized charge-reversal PAH-cit polymer. DOX@PAH-cit–BNNS complexes were prepared via step-by-step electrostatic interactions and were fully characterized. The cellular uptake of DOX@PAH-cit–BNNS complexes and DOX release inside cancer cells were visualized by confocal laser scanning microscopy. The in vitro anticancer activity of DOX@ PAH-cit–BNNS was examined using CCK-8 and live/dead viability/cytotoxicity assay.ResultsThe PAH-cit–BNNS complexes were nontoxic to normal and cancer cells up to a concentration of 100 µg/mL. DOX was loaded on PAH-cit–BNNS complexes with high efficiency. In a neutral environment, the DOX@PAH-cit–BNNS was stable, whereas the loaded DOX was effectively released from these complexes at low pH condition due to amide hydrolysis of PAH-cit. Enhanced cellular uptake of DOX@PAH-cit–BNNS complexes and DOX release in the nucleus of cancer cells were revealed by confocal microscopy. Additionally, the effective delivery and release of DOX into the nucleus of cancer cells led to high therapeutic efficiency.ConclusionOur findings indicated that the newly developed PAH-cit–BNNS complexes are promising as an efficient pH-responsive DDS for cancer therapy.

PH-Sensitive Zwitterionic Polymer as an Antimicrobial Agent with Effective Bacterial Targeting.

It is highly desirable to develop new and more potent biocompatible antimicrobial agents to reduce the increasing risk of bacterial infection worldwide. To address this problem, we prepared a smart pH-sensitive polymer, poly(N'-citraconyl-2-(3-aminopropyl-N,N-dimethylammonium)ethyl methacrylate), or P(CitAPDMAEMA), which can undergo change in functionality from a biocompatible zwitterionic polymer to an antimicrobial cationic polymer at acidic bacterial infection sites. The precursor polymer, poly(2-(3-aminopropyl-N,N-dimethylammonium)ethyl methacrylate) (P(APDMAEMA)), was first prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization, and then modified with citraconic anhydride to obtain the zwitterionic P(CitAPDMAEMA). P(CitAPDMAEMA) is zwitterionic at physiological pH and exhibits low hemotoxicity and good biocompatibility. However, P(CitAPDMAEMA) can change from neutral to cationic with decreasing pH because of the hydrolysis of citraconic amide under low pH conditions. This switch leads to pronounced bacteria binding of cationic P(CitAPDMAEMA) under acidic conditions of the infection sites and significantly inhibits the growth of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). These results indicate that P(CitAPDMAEMA) is potentially a new on-demand antimicrobial agent.