Cleavage Of Amide Bond Research Articles

Selective C-C bond cleavage of amides fused to 8-aminoquinoline controlled by a catalyst and an oxidant.

Herein, copper-catalyzed direct C-C bond cleavage of amides fused to 8-aminoquinoline as a directing group to form urea in the presence of amines and dioxygen is reported. Compared to the previous C-H aminations of amides via C-H activation, this reaction presents a catalyst and oxidant controlled C-C bond cleavage strategy that enables amidation through a radical process. CuBr/Ag2CO3/O2 shows the best catalytic result at 150 °C. A series of aryl and alkyl amides were compatible with this transformation. Notably, this method provided access to cyclohexanone, one of the most important industrial materials. The pathway of this reaction was investigated.

Insight into nucleophilic fragmentation mechanisms by glutamic acid side chain in singly protonated glutathione and related peptidyl ions.

Fragmentation mechanisms of the singly protonated glutathione (γ-ECG) and its synthetic analogue peptides (ECG and PPECG) have been investigated by liquid chromatography tandem-mass spectrometry and theoretical calculations. In the mass spectra, similar fragmentation patterns were observed for γ-ECG and ECG, but a completely different one was found in the case of PPECG. The E-C amide bond cleavage is the predominant pathway for the fragmentation of γ-ECG and ECG, whereas the additional N-terminal prolyl residues in PPECG significantly suppress the E-C amide bond cleavage. Theoretical calculations reveal that the fragmentation efficiencies of the E-C bonds in the protonated γ-ECG and ECG are much higher than that in the protonated PPECG, being attributed to their lower barriers of the potential energy; clearly the introduction of two prolyl residues can increase substantially the potential energy barrier. In the proposed mechanism, the protonated E-C amide bonds in the three peptides are first weakened followed by a nucleophilic addition by the glutamyl carboxyl oxygen atom in side chain, leading to the breaking of the E-C amide bonds. However, the processes of E-C bond fragmentation for three protonated analogs were not collaborative. Protonated amide bonds first fragment, then the nucleophilic addition by the side chain of glutamyl carboxyl oxygen atom takes places. On the other hand, the prolyl residues in PPECG can largely diminish the nucleophilic addition, resulting in a much lower efficiency of its E-C amide bond breaking. Distance analysis indicates that breaking the E-C amide bonds in the protonated γ-ECG, ECG, and PPECG ions could not occur without the assistance from the nucleophilic attack, highlighting an asynchronous collaborative process in the bond breakings.

Application of the Cleavable Isocyanide in Efficient Approach to Pyroglutamic Acid Analogues with Potential Biological Activity

Two efficient procedures have been developed for the synthesis of pyroglutamic acid analogues 28, 29, and 34. According to the first method the Ugi (4C3C) reaction is followed by a post-transformation reaction, and the second method involves the Michael addition reaction. The present methodologies demonstrate the applicability of 1-(2,2-dimethoxyethyl)-2-isocyanobenzene (15) as a cleavable isocyanide in the Ugi/ post-transformation reaction and a strong nucleophile in the Michael addition reaction. The framework of pyroglutamic acid analogues has been constructed by the selective cleavage of the C-terminal amide bond and nucleophilic addition to the activated α,β-unsaturated carbonyl group.

Continuous Activity Assay for HDAC11 Enabling Reevaluation of HDAC Inhibitors.

Histone deacetylase 11 (HDAC11) preferentially removes fatty acid residues from lysine side chains in a peptide or protein environment. Here, we report the development and validation of a continuous fluorescence-based activity assay using an internally quenched TNFα-derived peptide derivative as a substrate. The threonine residue in the +1 position was replaced by the quencher amino acid 3′-nitro-l-tyrosine and the fatty acyl moiety substituted by 2-aminobenzoylated 11-aminoundecanoic acid. The resulting peptide substrate enables fluorescence-based direct and continuous readout of HDAC11-mediated amide bond cleavage fully compatible with high-throughput screening formats. The Z′-factor is higher than 0.85 for the 15 μM substrate concentration, and the signal-to-noise ratio exceeds 150 for 384-well plates. In the absence of NAD+, this substrate is specific for HDAC11. Reevaluation of inhibitory data using our novel assay revealed limited potency and selectivity of known HDAC inhibitors, including Elevenostat, a putative HDAC11-specific inhibitor.

Doubly Charged Small Organic Fragments Derived from [Ce(tripeptide)(CH3CN)m]3+ Complexes: Observation of the Elusive [bn + H]2+ Ions.

[a3 + H]2+ ions generated from Ln3+/tripeptide complexes, where Ln = La or Ce, have similar structures to the linear [an]+ ions but with protonation at both the terminal NH2 and N═CH2 groups. Ion stability is favored by having the basic secondary amine of the proline residue at the N-terminus and by an amino acid residue accommodating one of the protons on the side chain. Dissociation of [a3 + H]2+ ions derived from peptides containing only aliphatic residues is by cleavage of the second amide bond to give [b2]+ or [a2]+ ions along with internal [a1]+ ions. For [a3 + H]2+ ions containing a tryptophan residue in the central location, in addition to cleavage of the amide bond, losses of neutrals NH3, HN═CHR, (NH3 + CO), and HNCO were observed. Dissociations of some unsolvated Ln3+/tripeptide complexes gave [b3 + H]2+ ions in low abundance; formation of these [b3 + H]2+ ions was favored by the presence of a proline residue at the N-terminus and by either a histidine or tryptophan residue in the central position. Dissociation of these [b3 + H]2+ ions was by the loss of (H2O + CO) and not only CO, indicating that these ions did not have the same type of oxazolone structure as found for [bn]+ ions. Density functional theory calculations suggest that the observed [b3 + H]2+ ions of ProGlyGly were formed from [Ce(ProGlyGly)]3+ complexes in which the peptide was bound to the metal ion as an enolate. Dissociation of the slightly lower-energy complex, where the peptide is bound in the keto form, would produce an oxazolone but the high barrier required to create this isomer of the [b3 + H]2+ ion would be sufficient to result in further dissociation. Two isomers of the [b3 + H]2+ ion of ProHisGly have been created, one from the [Ce(ProHisGly)]3+ complex that characteristically dissociates by the combined loss of (H2O + CO) and the other by the loss of glycine from [ProHisGlyGly + 2H]2+. The [b3 + H]2+ ion derived from [ProHisGlyGly + 2H]2+ dissociated by the loss of only CO.

Parallel profiling of an enzyme family

Metabolomics Uncharacterized gene sequences are annotated based on the function of distant relatives and often have very different functions in reality. Kim et al. developed a method based on untargeted metabolomics to fill in the gaps and assign precise function to members of the M20 peptidase family, which generally catalyze amide bond cleavage. Viral transduction of each enzyme in mice and comparative analysis of levels of metabolites in liver tissue recovered known enzyme functions for two family members and assigned a new function, dipeptide cleavage, for one of the orphan enzymes in this family. Cell Chem. Biol. 10.1016/j.chembiol.2019.09.009 (2019).

Na2CO3-promoted thioesterification via N–C bond cleavage of amides to construct thioester derivatives

A mild, efficient, and transition-metal-free catalytic strategy is developed to construct thioesters via selective N–C bond cleavage of Boc2-activated primary amides. This strategy is successfully carried out with stoichiometric Na2CO3 as the base and provides the corresponding products in moderate to excellent yields.

Structures and Dissociation Products of Ce/Peptide Complexes: Competition between Coordination and Charge Delocalization.

Structures of [Ce(GGG)]3+ and [Ce(GGG ? H)]2+ have been investigated by DFT calculations. The two lowest-energy structures of the triply charged metal complex have the peptide in either the iminol or conventional zwitterionic form, and these ions have almost identical energies. In the doubly charged complex, the iminol and charge-solvated structures are the best structures on the potential energy surface, but the latter is favored. In both iminol structures, the metal ion coordinates to the iminol oxygen rather than to the nitrogen, unlike in previously reported iminol-containing complexes. Triply charged [Ce(peptide)]3+ complexes are fragile and not easily isolated in a mass spectrometer, whereas the doubly charged [Ce(peptide ? H)]2+ complexes are more robust. Here, we studied the fragmentations of 37 [Ce(peptide ? H)]2+ and 30 [Ce(peptide)(peptide ? H)]2+ complexes and the results are systematically summarized. Losses of CO and/or H2O are the most commonly observed fragmentation channels for [Ce(peptide ? H)]2+ complexes and these dissociation pathways are modeled by DFT calculations. For [Ce(peptide)(peptide ? H)]2+ complexes the neutral peptide plays the role of a solvent molecule but, unlike in the dissociations of [Ce(CH3CN)(peptide ? H)]2+ complexes, the loss of the solvent molecule is not observed. Instead, fragmentation occurs by cleavage of the second amide bond of the solvating peptide molecule.

Cleavable Amide Bond: Mechanistic Insight into Cleavable 4-Aminopyrazolyloxy Acetamide at Low pH.

The cleavage of amide bonds under mild acidic conditions is a rare chemical event. N-Acetamide bond of peptides is extremely stable even under the strongest organic acid trifluoromethanesulfonic acid. This report mechanistically describes a new cleavable amide bond in 4-aminopyrazolyloxy acetamide peptide analogues under mild acidic conditions such as trifluoroacetic acid (10-20%) or HCl (0.1-4.0 N) at room temperature, and the formation of unusual lactam from 4-aminopyrazolyloxy acetic acid after evaporation of solvent. This is a rare chemical event in peptide bond, which could be explored as acid-sensitive protecting group of free amines.

Breaking Amide C-N Bonds in an Undergraduate Organic Chemistry Laboratory.

An undergraduate organic chemistry laboratory experiment involving the breakage of amide C-N bonds is reported. Whereas amides are typically considered stable species due to well-established resonance effects, this experiment allows students to cleave the amide C-N bond in a nickel-catalyzed esterification process. Moreover, students perform the experiment on the benchtop using a commercially available paraffin wax capsule containing the necessary nickel precatalyst and N-heterocyclic carbene ligand. The laboratory procedure introduces students to several modern topics in organic chemistry that are not otherwise well-represented in typical undergraduate organic chemistry curricula, such as amide bond cleavage, transition metal-catalyzed cross-coupling reactions, and nonprecious-metal catalysis.

Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage.

Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.

Triflamides: Highly Reactive, Electronically Activated N-Sulfonyl Amides in Catalytic N-C(O) Amide Cross-Coupling.

The direct, highly chemoselective Suzuki-Miyaura cross-coupling of trifluoromethanesulfonamides (triflamides) by selective N-C(O) amide bond cleavage is reported. This operationally simple, mild, and user-friendly method accomplishes the direct synthesis of ketones from amides by a catalytic manifold as a powerful alternative to Weinreb amides. Mechanistic studies support rotational inversion and electronic activation, favoring selective insertion under mild conditions. Our data strongly suggest that triflamides should be routinely considered as precursors in amide bond cross-coupling.

Weinreb Amide as Secondary Station for the Dibenzo‐24‐crown‐8 in a Molecular Shuttle

Here is reported the synthesis of a new molecular shuttle: it consists of a dibenzo‐24‐crown‐8 (DB24C8) that surrounds a molecular axle containing an ammonium group and a newly considered Weinreb amide as stations. At the protonated state the DB24C8 is localized around the best ammonium station, while deprotonation‐carbamoylation of the ammonium triggers the shuttling of the macrocycle around the Weinreb amide site. Further post‐interlocking modification of the [2]rotaxane was attempted through the cleavage of the Weinreb amide bond using a Grignard reagent. While the non‐interlocked molecular axle was cleaved after a short time in mild conditions, the Weinreb amide bond remained unaltered in the [2]rotaxane species over time, even in the presence of a larger amount of Grignard and at a higher temperature, highlighting the protection shield of the macrocycle around the encircled axle.

Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group-A Model for yet Unknown Peptidases?

Unconstrained amides that undergo fast hydrolysis under mild conditions are valuable sources of information about how amide bonds may be activated in enzymatic transformations. We report a compound possessing an unconstrained amide bond surrounded by an amino and a carboxyl group, each mounted in close proximity on a bicyclic scaffold. Fast amide hydrolysis of this model compound was found to depend on the presence of both the amino and carboxyl functions, and to involve a proton transfer in the rate-limiting step. Possible mechanisms for the hydrolytic cleavage and their relevance to peptide bond cleavage catalyzed by natural enzymes are discussed. Experimental observations suggest that the most probable mechanisms of the model compound hydrolysis might include a twisted amide intermediate and a rate-determining proton transfer.

Well-Defined Pre-Catalysts in Amide and Ester Bond Activation.

Over the past few decades, transition metal catalysis has witnessed a rapid and extensive development. The discovery and development of cross-coupling reactions is considered to be one of the most important advancements in the field of organic synthesis. The design and synthesis of well-defined and bench-stable transition metal pre-catalysts provide a significant improvement over the current catalytic systems in cross-coupling reactions, avoiding excess use of expensive ligands and harsh conditions for the synthesis of pharmaceuticals, agrochemicals and materials. Among various well-defined pre-catalysts, the use of Pd(II)-NHC, particularly, provided new avenues to expand the scope of cross-coupling reactions incorporating unreactive electrophiles, such as amides and esters. The strong σ-donation and tunable steric bulk of NHC ligands in Pd-NHC complexes facilitate oxidative addition and reductive elimination steps enabling the cross-coupling of broad range of amides and esters using facile conditions contrary to the arduous conditions employed under traditional catalytic conditions. Owing to the favorable catalytic activity of Pd-NHC catalysts, a tremendous progress was made in their utilization for cross-coupling reactions via selective acyl C–X (X=N, O) bond cleavage. This review highlights the recent advances made in the utilization of well-defined pre-catalysts for C–C and C–N bond forming reactions via selective amide and ester bond cleavage.

Energetic switch of the proline effect in collision‐induced dissociation of singly and doubly protonated peptide Ala‐Ala‐Arg‐Pro‐Ala‐Ala

Suppression of the selective cleavage at N-terminal of proline is observed in the peptide cleavage by proteolytic enzyme trypsin and in the fragment ion mass spectra of peptides containing Arg-Pro sequence. An insight into the fragmentation mechanism of the influence of arginine residue on the proline effect can help in prediction of mass spectra and in protein structure analysis. In this work, collision-induced dissociation spectra of singly and doubly charged peptide AARPAA were studied by ESI MS/MS and theoretical calculation methods. The proline effect was evaluated by comparing the experimental ratio of fragments originated from cleavage of different amide bonds. The results revealed that the backbone amide bond cleavage was selected by the energy barrier height of the fragmentation pathway although the strong proton affinity of the Arg side chain affected the stereostructure of the peptide and the dissociation mechanism. The thermodynamic stability of the fragment ions played a secondary role in the abundance ratio of fragments generated via different pathways. Fragmentation studies of protonated peptide AACitPAA supported the energy-dependent hypothesis. The results provide an explanation to the long-term arguments between the steric conflict and the proton mobility mechanisms of proline effect.

Understanding the chlorination mechanism and the chlorine-induced separation performance evolution of polypiperazine-amide nanofiltration membrane

Although the tertiary amide bonds are quite stable to oxidants, the typical polypiperazine-amide (PPA) nanofiltration membranes (NFMs) were still reported to be susceptible to chlorine degradation. However, the understanding of the chlorination mechanism and the chlorine-induced separation performance evolution of the PPA NFMs still remains incomplete, significantly limiting the development of chlorine-resistant NFMs. In this work, two types of self-made PPA NFMs with different physicochemical structures and separation performance were employed to investigate the chlorination processes. The regeneration behaviour of the chlorinated PPA NFMs was studied for the first time. Our results indicated that the deterioration of the PPA separating layer upon chlorine exposure follows two pathways: reversible chlorine substitution of the -NH group to -NCl group, and oxidation of the -NH group to imine group. Part of the -NCl groups could be reduced to -NH groups during the regeneration process. No cleavage of tertiary amide bonds in the PPA polymer occurred. Separation performance evolution of the PPA NFMs after chlorination or regeneration was mainly induced by the variation of -NH group content in the PPA separating layer. The loss of -NH groups after chlorination and the reformation of -NH groups after regeneration could not only affect the density of the PPA separating layer through hydrogen bonds but also the electrostatic interaction between the PPA separating layer and ions. Additionally, the regenerated PPA NFMs showed good stability under elevated pressure or continuous filtration.

Insights into the synergetic mechanism of a combined vis-RGO/TiO2/peroxodisulfate system for the degradation of PPCPs: Kinetics, environmental factors and products

In recent years, how to effectively remove emerging organic pollutants in water bodies has been studied extensively, especially in the actual complex water environment. In the present study, an effective wastewater treatment system that combined photocatalysis and an oxidizing agent was investigated. Specifically, visible-light driven reduced graphene oxide (RGO)/TiO2 composites were prepared, and peroxodisulfate (PDS) was used as electron acceptor to accelerate the photocatalytic activity of this material. The vis-RGO/TiO2/PDS system exhibited outstanding properties in the degradation of diclofenac (DCF), which was also facilitated by acidic conditions and Cl−. Lake water, tap water, river water and HCO3− decreased the DCF degradation rate, while NO3− affected the system only slightly. Low concentrations of fulvic acid (FA) promoted the degradation of DCF via the generation of excited states, whereas a high concentration of FA inhibited the degradation, which was likely due to the light screening effect. The photocatalytic mechanism revealed that PDS served as an electron acceptor for the promotion of electron-hole pair separation and the generation of additional reactive oxygen species, while the RGO served as an electric conductor. The active substances, h+, OH, 1O2, SO4- and O2- were generated in this system, O2- and h+ played significant roles in the degradation of DCF based electron spin resonance tests and radical quenching results. According to the mass spectrometry results, the amide bond cleavage, dechlorination reaction, hydroxyl addition reaction, and decarboxylation reaction were the primary transformative pathways.

Synthesis of Gemcitabine-Threonine Amide Prodrug Effective on Pancreatic Cancer Cells with Improved Pharmacokinetic Properties.

To investigate the amino acid transporter-based prodrug anticancer strategy further, several amino acid-conjugated amide gemcitabine prodrugs were synthesized to target amino acid transporters in pancreatic cancer cells. The structures of the synthesized amino acid-conjugated prodrugs were confirmed by 1H-NMR and LC-MS. The pancreatic cancer cells, AsPC1, BxPC-3, PANC-1 and MIAPaCa-2, appeared to overexpress the amino acid transporter LAT-1 by conventional RT-PCR. Among the six amino acid derivatives of gemcitabine, threonine derivative of gemcitabine (Gem-Thr) was more effective than free gemcitabine in the pancreatic cancer cells, BxPC-3 and MIAPaCa-2, respectively, in terms of anti-cancer effects. Furthermore, Gem-Thr was metabolically stable in PBS (pH 7.4), rat plasma and liver microsomal fractions. When Gem-Thr was administered to rats at 4 mg/kg i.v., Gem-Thr was found to be successfully converted to gemcitabine via amide bond cleavage. Moreover, the Gem-Thr showed the increased systemic exposure of formed gemcitabine by 1.83-fold, compared to free gemcitabine treatment, due to the significantly decreased total clearance (0.60 vs. 4.23 mL/min/kg), indicating that the amide prodrug approach improves the metabolic stability of gemcitabine in vivo. Taken together, the amino acid transporter-targeting gemcitabine prodrug, Gem-Thr, was found to be effective on pancreatic cancer cells and to offer an efficient potential means of treating pancreatic cancer with significantly better pharmacokinetic characteristics than gemcitabine.

Imidazolone formation from protonated tetrapeptides: Effects of replacing a glycine by an alanine or proline residue

The propensity for water loss in protonated tetrapeptides that contain a hetero-residue in addition to glycines is examined. Protonated tetraglycine loses water prominently from its first amide group, with a minor contribution from the second amide group, to give a nominal [b4]+ ion. This chemistry is also apparent in protonated tetrapeptides that contain three glycine residues and one proline or alanine residue. When the alanine is at the N-terminus or in the third position of the peptide, abundances of the [b4]+ ions are low; when the alanine is in the second position, the abundance of [b4]+ ion is much higher, and is comparable to that obtained from tetraglycine. The [b4]+ ion is a protonated imidazolone formed by attack on the carbon of the first amide bond by the nitrogen of the third amide, both sites being partially obstructed by the methyl group of the alanine residue.All the [b4]+I ions (the Roman numeral refers to the residue from which the oxygen (water) was lost) dissociate by loss of an imine from the residue that is initially located at the N-terminus of the peptide. The [b4]+II ions dissociate by loss of either the imine from the second residue, via pre-dissociation rearrangement to a [b4]+I ion, or by loss of (imine plus CO) from the first residue; the latter involves a cleavage of the first amide bond. These dissociations follow the pathways observed for the protonated imidazolone ions derived from GlyGlyGlyGly. In addition to these losses, the [b4]+II ions of both GlyProGlyGly and GlyAlaGlyGly also lose HN = CH2 from the first residue, but only at higher collision energies. This requires that the [b4]+II ions rearrange to protonated imidazolones that bear an H2NCH2– group proximal to the imidazolone ring at the N-terminus, i.e., forming the [b4]+I ions of GlyProGlyGly and GlyAlaGlyGly. This rearrangement requires the transfer of an oxygen atom from the first amide group to the second α-carbon. Similarly, the [b4]+I ion of ProGlyGlyGly dissociates by loss of imines from both the first two residues; again loss of the ‘second’ imine, HN = CH2, only occurs at higher collision energies and requires rearrangement to the [b4]+I ion of GlyProGlyGly.