Methylamide Research Articles

Isofunctional but Structurally Different Methyltransferases for Dithiolopyrrolone Diversification

Dithiolopyrrolone (DTP) natural products are produced by several different bacteria and have potent antibacterial, antifungal and anticancer activities. While the amide of their DTP core can be methylated to fine‐tune bioactivity, the enzyme responsible for the amide N‐methylation has remained elusive in most taxa. Here, we identified the amide methyltransferase XrdM that is responsible for xenorhabdin (XRD) methylation in Xenorhabdus doucetiae but encoded outside of the XRD gene cluster. XrdM turned out to be isofunctional with the recently reported methyltransferase DtpM, that is involved in the biosynthesis of the DTP thiolutin, although its X‐ray structure is unrelated to that of DtpM. To investigate the structural basis for ligand binding in both enzymes, we used X‐ray crystallography, modeling, site‐directed mutagenesis, and kinetic activity assays. Our study expands the limited knowledge of post‐non‐ribosomal peptide synthetase (NRPS) amide methylation in DTP biosynthesis and reveals an example of convergent evolution of two structurally completely different enzymes for the same reaction in different organisms.

Understanding structure/rheology relationships of amidated low-methoxyl citrus and apple pectin gels: Implications of sucrose, pectin types and characteristics

In this study, the relationships between structure and rheology (at small and large deformations) of amidated low-methoxyl (LMA) citrus and apple pectin gels were investigated considering how does these relationships can be modulated by soluble solids (sucrose), pectin types and characteristics. For that purpose, various LMA pectins with varying degrees of methyl esterification (DE) and amidation (DA), processed from citrus peels and apple pomace, were used. Scaling models of biopolymer gels have been critically discussed in respect to pectin critical gelling concentration (C0) and their structural variabilities. It was demonstrated that, whatever the types of LMA pectins and their structural variabilities, scalar percolation and quadratic models can be efficiently used for the prediction of the storage modulus G′ and C0 as other biopolymer gels. Fractal approach reveals that the origin of the LMA pectin gel elasticity is more in harmony with an enthalpic network of rod-like filaments with bending rigidity ruling the network's elasticity. The addition of sucrose induced an anticipation of the gelation temperature and an important improvement of the viscoelastic properties of the resulting gels. It was also shown that the most tough gels are obtained for citrus pectins due to the higher level of neutral sugar side chains in apple pectins that can hinder preponderant ca-bridging sites unlike citrus pectins. Finally, it was shown that unlike the firmness and hardness of the gels which appear to be more driven by the amide groups, the deformability of the gels is rather governed by the methyl ester groups.

Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model.

Accurate parametrization of amino acids is pivotal for the development of reliable force fields for molecular modeling of biomolecules such as proteins. This study aims to assess amino acid electrostatic parametrizations with the polarizable Gaussian Multipole (pGM) model by evaluating the performance of the pGM-perm (with atomic permanent dipoles) and pGM-ind (without atomic permanent dipoles) variants compared to the traditional RESP model. The 100-conf-combterm fitting strategy on tetrapeptides was adopted, in which (1) all peptide bond atoms (-CO-NH-) share identical set of parameters and (2) the total charges of the two terminal N-acetyl (ACE) and N-methylamide (NME) groups were set to neutral. The accuracy and transferability of electrostatic parameters across peptides with varying lengths and real-world examples were examined. The results demonstrate the enhanced performance of the pGM-perm model in accurately representing the electrostatic properties of amino acids. This insight underscores the potential of the pGM-perm model and the 100-conf-combterm strategy for the future development of the pGM force field.

Trans-3-Benzyloxycarbonylamino-1-methyl-3-(methylcarbamoyl)azetidine-1-oxide

trans-3-Benzyloxycarbonylamino-1-methyl-3-(methylcarbamoyl)azetidine-1-oxide was prepared by stereoselective oxidation of the corresponding azetidine precursor. The stable molecule was characterized in a low-polarity solution by IR, 1H-NMR and 13C-NMR, and in the solid state as a co-crystal with water by X-Ray diffraction. The N-oxide function made a strong intramolecular 7-membered ring hydrogen bond with the methyl amide NH in solution and formed an intermolecular H-bond with the carbamate NH in a neighboring molecule in the solid state.

DNA-Compatible Conditions for the Formation of N-Methyl Peptide Bonds.

DNA-encoded libraries (DELs) are a powerful platform in drug discovery. Peptides have unique properties that make them attractive pharmaceutical candidates. N-methylation of the peptide backbone can confer beneficial properties such as increased proteolytic stability and membrane permeability. Herein, we evaluate different DEL reaction systems and report a DNA-compatible protocol for forming N-methylated amide bonds. The DNA-compatible, bis(trichloromethyl)carbonate-mediated amide coupling is efficient for the formation of N-methyl peptide bonds, which promises to increase the opportunity to identify passively cell-permeable macrocyclic peptide hits by DNA-encoded technology.

Peptide Cyclization by the Use of Acylammonium Species.

Although cyclic peptides have become increasingly important as drugs, the most conventional peptide cyclization method using moderately active coupling agents suffers from a lot of waste and high cost as well as long reaction times and burdensome purification. Herein, we report an unconventional approach to peptide cyclization that uses acylammonium species generated from inexpensive and less wasteful Me2 NBn and ClCO2 i-Pr. Using this approach, we observed the desired rapid activation of the C-terminus of cyclization precursors by an acylammonium ion for rapid and epimerization/dimerization-free cyclization of synthetically challenging peptides, including a difficult cyclization involving N-methyl amide bond formation. The ease of purification, productivities, and reaction mass efficiencies of our approach were significantly superior to those in previous reports. We synthesized a previously reported versicotide D analogue, and our data indicated that its assigned stereostructure should be revised.

Novel Allosteric Effectors Targeting Human Transcription Factor TEAD.

The Hippo pathway is an evolutionary conserved signaling network involved in several cellular regulatory processes. Dephosphorylation and overexpression of Yes-associated proteins (YAPs) in the Hippo-off state are common in several types of solid tumors. YAP overexpression results in its nuclear translocation and interaction with transcriptional enhanced associate domain 1-4 (TEAD1-4) transcription factors. Covalent and non-covalent inhibitors have been developed to target several interaction sites between TEAD and YAP. The most targeted and effective site for these developed inhibitors is the palmitate-binding pocket in the TEAD1-4 proteins. Screening of a DNA-encoded library against the TEAD central pocket was performed experimentally to identify six new allosteric inhibitors. Inspired by the structure of the TED-347 inhibitor, chemical modification was performed on the original inhibitors by replacing secondary methyl amide with a chloromethyl ketone moiety. Various computational tools, including molecular dynamics, free energy perturbation, and Markov state model analysis, were employed to study the effect of ligand binding on the protein conformational space. Four of the six modified ligands were associated with enhanced allosteric communication between the TEAD4 and YAP1 domains indicated by the relative free energy perturbation to original molecules. Phe229, Thr332, Ile374, and Ile395 residues were revealed to be essential for the effective binding of the inhibitors.

Rimonabant-Based Compounds Bearing Hydrophobic Amino Acid Derivatives as Cannabinoid Receptor Subtype 1 Ligands.

In this study, 1H-pyrazole-3-carboxylic acids related to the cannabinoid type 1 (CB1) receptor antagonist rimonabant were amidated with valine or tert-leucine, and the resulting acids were further diversified as methyl esters, amides, and N-methyl amides. In vitro receptor binding and functional assays demonstrated a wide series of activities related to the CB1 receptors (CB1Rs). Compound 34 showed a high CB1R binding affinity (K i = 6.9 nM) and agonist activity (EC50 = 46 nM; E max = 135%). Radioligand binding and [35S]GTPγS binding assays also demonstrated its selectivity and specificity to CB1Rs. Moreover, in vivo experiments revealed that 34 was slightly more effective than the CB1 agonist WIN55,212-2 in the early phase of the formalin test, indicating a short duration of the analgesic effect. Interestingly, in a mouse model of zymosan-induced hindlimb edema, 34 was able to maintain the percentage of paw volume below 75% for 24 h following subcutaneous injection. After intraperitoneal administration, 34 increased the food intake of mice, suggesting potential activity on CB1Rs.

Preparation of polyacrylamide-poly(methyl methacrylate) emulsion for enhancing the adhesion of polyester/cotton yarn

Polyacrylamide-poly(methyl methacrylate) copolymer emulsion was synthesized by prepolymerization of methyl methacrylate, and then copolymerization with acrylamide. The final yield of polyacrylamide-poly(methyl methacrylate) emulsion can be up to 93.69%, and its molecular weight was 11.2 × 104 Da, as well as the characteristic peaks of the ester group (–COO) of methyl methacrylate and amide group (–NH2) of acrylamide appeared on its structure. The component content of acrylamide and methyl methacrylate from polyacrylamide-poly(methyl methacrylate) can be effectively controlled by adjusting the prepolymerization conversion of methyl methacrylate. The polyacrylamide-poly(methyl methacrylate) emulsion exhibited spherical morphology, and its particle size was 50–130 nm. Moreover, the correlation between particle size and the film-forming property of the polyacrylamide-poly(methyl methacrylate) emulsion was studied. It was concluded that when the particle size was small, the aggregation ability among molecules was strong, and endowed polyacrylamide-poly(methyl methacrylate) emulsion film with more action during the stretching process, making it able to withstand the larger tensile opposite force. Interestingly, the polyacrylamide-poly(methyl methacrylate) emulsion can reinforce the adhesion of polyester/cotton yarn. These benefit from the strong hydrogen bond between polyacrylamide and cotton yarn and poly(methyl methacrylate) had a similar ester structure to polyester fibers. This work solves the problems of difficult copolymerization between acrylamide and acrylate, it provides a new way to develop acrylamide-based copolymer adhesive.

Visible‐light Induced Cerium‐catalyzed N‐Demethylation of N‐Methyl Amides under Air Conditions

AbstractA visible‐light induced cerium‐catalyzed N‐demethylation of N‐methyl amides under air atmosphere to the corresponding of N‐demethylated amides is presented. Upon irradiation the excited states of [CeIVCln]2− are able to activate N‐methyl amides. This reaction provides a methodology to cleave the C−N bond of amides under air conditions.magnified image

Cu-Catalyzed Methylenation of Alcohols with N-Methyl Amide as a Sustainable Methylene Reagent

Herein, we report a new approach to methylenation of alcohols using N-methyl amide as a sustainable methylene reagent; the N-methyl delivers the methylene group. This new reagent is easily prepared and stable to both air and moisture. Furthermore, the final byproduct of this methylene reagent can be recycled in excellent yields and then reused in methylenation reactions upon treating with CH3I.

Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions.

Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.

Research of a novel fracturing-production integral fluid based on cationic surfactant

Fracturing plays an extremely important role in increasing oil and gas production, however, the fracturing flowback fluid has problems such as large volume, difficult treatment, high processing cost, and environmental pollution. In order to expand the application range and reuse of clean fracturing fluid,a fracturing-production integral fluid based on small molecule surfactants, cetyl trimethyl ammonium chloride (CTAC), salicylic acid (SA) and oleic acid amide methyl hydroxypropyl ammonium chloride (OAMDC) is proposed. At 90 °C the resistance of the fracturing-production integral fluid reached values up to 63.5 mPa·s. The surface and interface tension of the fracturing-production integral fluid broken by crude oil were 28.5 and 8.19 × 10-3 mN/m, respectively. It shows good oil flooding ability (up to 16.35 %), static oil washing rate (up to 21.5 %) and outstanding emulsification effect. Meanwhile, the application scope clean fracturing flowback fluid will be expanded to achieve its efficient and comprehensive application in the field of oilfield chemistry, thereby improving the benefits of oilfield development.

Integrative Strategy for Investigating the Interactions between STING and Small-Molecule Ligands.

Although small-molecule agonists of stimulator of interferon genes (STING) show significance in activating the immune system, the dynamic process involved in ligands activating STING remains unclear. Herein, we developed a biochemical strategy, integrating computer simulation and a biochemical engineering approach, to reveal the interaction mechanism between STING and 5,6-dimethylxanthenone-4-acetic acid (DMXAA), an agonist that activates the TANK binding kinase 1-interferon regulatory factor 3 signaling pathway. Specifically, inspired by an analysis of the STING-DMXAA crystal structure, we designed and synthesized DMXAA derivatives to investigate the STING-DMXAA binding model. We identified that the carboxyl moiety of DMXAA was a major pharmacophore responsive to STING activation. In particular, the loss of hydrogen bond interaction between the carboxylic acid of DMXAA and the side chain Thr262 of STING led to STING inhibition. DMXAA N-methyl amide derivative (DNHM) exhibited good inhibitor activity, inhibited STING-mediated interferon production in vitro and in vivo, and effectively attenuated STING-associated inflammatory diseases. Therefore, we provide a new insight into STING-ligand interactions, which may improve the understanding of STING biology.

Structure-Activity Relationships for the N-Me- Versus N-H-Amide Modification to Macrocyclic ent-Verticilide Antiarrhythmics.

The synthesis of all N-Me and N-H analogues of ent-verticilide is described, enabling a structure-activity relationship study based on cardiac ryanodine receptor (RyR2) calcium ion channel inhibition. The use of permeabilized cardiomyocytes allowed us to correlate the degree of N-methylation with activity without concern for changes in passive membrane permeability that these modifications can cause. A key hypothesis was that the minimal pharmacophore may be repeated in this cyclic oligomeric octadepsipeptide (a 24-membered macrocycle), opening the possibility that target engagement will not necessarily be lost with a single N-Me → N-H modification. The effect in the corresponding 18-membered ring oligomer (ent-verticilide B1) was also investigated. We report here that a high degree of N-methyl amide content is critical for activity in the ent-verticilide series but not entirely so for the ent-verticilide B1 series.

Life sciences discovery and technology highlights

Life sciences discovery and technology highlights

Photoinduced C(sp3)-H Chalcogenation of Amide Derivatives and Ethers via Ligand-to-Metal Charge-Transfer.

A photoinduced, iron(III) chloride-catalyzed C-H activation of N-methyl amides and ethers leads to the formation of C-S and C-Se bonds via a ligand-to-metal charge transfer (LMCT) process. This methodology converts secondary and tertiary amides, sulfonamides, and carbamates into the corresponding amido-N,S-acetal derivatives in good yields. Mechanistic work revealed that this transformation proceeds through a hydrogen atom transfer (HAT) involving chlorine radical intermediates.

The lipophilic cyclic peptide cyclosporin A induces aggregation of gel-forming mucins

Cyclic peptides are good candidates for orally delivered therapeutics, however, issues remain in their development due to low intestinal permeability. Although some of the biological factors have been reported that regulate intestinal permeation of cyclic peptides, the influence of the mucus barrier, a major hurdle to epithelial drug delivery, on cyclic peptide bioavailability is unclear. In this study, we show that the lipophilic cyclic peptide, cyclosporin A (CsA), interacted with, and likely induced aggregation, of polymeric, gel-forming mucins (MUC2, MUC5AC and MUC5B) which underpin the mucus gel-networks in the gastrointestinal tract. Under similar conditions, two other cyclic peptides (daptomycin and polymyxin B) did not cause mucin aggregation. Using rate-zonal centrifugation, purified MUC2, MUC5AC and MUC5B mucins sedimented faster in the presence of CsA, with a significant increase in mucins in the pellet fraction. In contrast, mucin sedimentation profiles were largely unaltered after treatment with daptomycin or polymyxin B. CsA increased MUC5B sedimentation was concentration-dependent, and sedimentation studies using recombinant mucin protein domains suggests CsA most likely causes aggregation of the relatively non-O-glycosylated N-terminal and C-terminal regions of MUC5B. Furthermore, the aggregation of the N-terminal region, but not the C-terminal region, was affected by pH. CsA has partially N-methylated amide groups, this unique molecular structure, not present in daptomycin and polymyxin B, may potentially be involved in interaction with gel-forming mucin. Taken together, our results indicate that the interaction of gel-forming mucins with the cyclic peptide CsA is mediated at the N- and C-terminal domains of mucin polymers under physiological conditions. Our findings demonstrate that the mucus barrier is an important physiological factor regulating the intestinal permeation of cyclic peptides in vivo.

Drug-like molecules with anti-trypanothione synthetase activity identified by high throughput screening

Trypanothione synthetase (TryS) catalyses the synthesis of N 1 ,N8 -bis(glutathionyl)spermidine (trypanothione), which is the main low molecular mass thiol supporting several redox functions in trypanosomatids. TryS attracts attention as molecular target for drug development against pathogens causing severe and fatal diseases in mammals. A drug discovery campaign aimed to identify and characterise new inhibitors of TryS with promising biological activity was conducted. A large compound library (n = 51,624), most of them bearing drug-like properties, was primarily screened against TryS from Trypanosoma brucei (TbTryS). With a true-hit rate of 0.056%, several of the TbTryS hits (IC50 from 1.2 to 36 µM) also targeted the homologue enzyme from Leishmania infantum and Trypanosoma cruzi (IC50 values from 2.6 to 40 µM). Calmidazolium chloride and Ebselen stand out for their multi-species anti-TryS activity at low µM concentrations (IC50 from 2.6 to 13.8 µM). The moieties carboxy piperidine amide and amide methyl thiazole phenyl were identified as novel TbTryS inhibitor scaffolds. Several of the TryS hits presented one-digit µM EC50 against T. cruzi and L. donovani amastigotes but proved cytotoxic against the human osteosarcoma and macrophage host cells (selectivity index ≤ 3). In contrast, seven hits showed a significantly higher selectivity against T. b. brucei (selectivity index from 11 to 182). Non-invasive redox assays confirmed that Ebselen, a multi-TryS inhibitor, induces an intracellular oxidative milieu in bloodstream T. b. brucei. Kinetic and mass spectrometry analysis revealed that Ebselen is a slow-binding inhibitor that modifies irreversible a highly conserved cysteine residue from the TryS’s synthetase domain. The most potent TbTryS inhibitor (a singleton containing an adamantine moiety) exerted a non-covalent, non-competitive (with any of the substrates) inhibition of the enzyme. These data feed the drug discovery pipeline for trypanosomatids with novel and valuable information on chemical entities with drug potential.

Macrocyclization and Backbone Modification in RiPP Biosynthesis.

The past decade has seen impressive advances in understanding the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). One of the most common modifications found in these natural products is macrocyclization, a strategy also used by medicinal chemists to improve metabolic stability and target affinity and specificity. Another tool of the peptide chemist, modification of the amides in a peptide backbone, has also been observed in RiPPs. This review discusses the molecular mechanisms of biosynthesis of a subset of macrocyclic RiPP families, chosen because of the unusual biochemistry involved: the five classes of lanthipeptides (thioether cyclization by Michael-type addition), sactipeptides and ranthipeptides (thioether cyclization by radical chemistry), thiopeptides (cyclization by [4+2] cycloaddition), and streptide (cyclization by radical C-C bond formation). In addition, the mechanisms of backbone amide methylation, backbone epimerization, and backbone thioamide formation are discussed, as well as an unusual route to small molecules by posttranslational modification.