A Small Change in Structure, a Big Change in Flexibility

Studies of the rotational barrier energy of the amide bond using quantum computing and nuclear magnetic resonance (NMR) are focused mainly on its use as a model of the peptide bond. The results of these studies are valuable not only in terms of the fundamental conformational properties of amide bonds, but also in the design of molecular machines, which have recently attracted interest. We investigate the fluxionality of the amide and enamide bonds of compound 3-[(E)-(dimethylamino)methylidene]-1,1-dimethylurea using advanced dynamic NMR experiments and a theoretical evaluation of the density functional theory (DFT) calculation. The dynamic NMR study shows restricted rotation around the amide group (16.4 kcal/mol) and a very high barrier around the enamine group (18.6 kcal/mol). In a structurally similar compound, (E)-3-(dimethylamino)-N,N-dimethylacrylamide (N atom is replaced by CH), the amide barrier is 12.4 kcal/mol and the enamine barrier is 11.7 kcal/mol. The DFT studies of both compounds reveal the electronic origin of this phenomenon. Theoretical calculations reveal the origin of the higher enamine barrier. The better delocalization of the lone pair of electrons on the end nitrogen atom into the antibonding orbital of the neighboring C-N double bond leads to the better stabilization of the ground state, and this leads to a greater increase in the enamine barrier.

Diacetyl strategy for synthesis of NHAc containing glycans: enhancing glycosylation reactivity via diacetyl imide protection

The presence of NHAc groups in the substrates (both glycosyl donors and acceptors) significantly reduced the reactivity of glycosylation. This decrease was attributed to the NHAc groups forming intermolecular hydrogen bonds by the NHAc groups, thereby reducing molecular mobility. Hence, a diacetyl strategy involving the temporary conversion of NHAc to diacetyl imide (NAc2) was developed for the synthesis of NHAc-containing glycans. This strategy has two significant advantages for oligosaccharide synthesis. The NAc2 protection of NHAc substantially enhances the rate of glycosylation reactions, resulting in improved yields. Moreover, NAc2 can be readily reverted to NHAc by the simple removal of one acetyl group under mild basic conditions, obviating the necessity for treating the polar amino group. We have achieved the efficient synthesis of oligosaccharides containing GlcNHAc and N-glycans containing sialic acid using the diacetyl strategy.

Recycling Compatible Organic Electrode Materials Containing Amide Bonds for Use in Rechargeable Batteries

Organic rechargeable batteries that do not use any scarce heavy metals are candidates for the next generation of rechargeable batteries; although, it is not easy to realize both high capacity and long cycle life. Organic compounds linked by amide bonds are expected to have superior recycling properties after battery degradation, since they will become a single monomer upon hydrolysis. In this study, anthraquinone was chosen as a model redox active unit, and dimeric and trimeric compounds were synthesized, their cycle performances as electrode materials for use in rechargeable batteries were compared, and a trend in which oligomerization improves cycle properties was confirmed. Furthermore, quantum chemistry calculations suggest that oligomerization decreases solubility, which would support a longer life for oligomerized compounds. This methodology will lead to the development of organic rechargeable batteries with further environmental benefits.

Screening of the active Ingredients in Huanglian Jiedu decoction through amide bond-Immobilized magnetic nanoparticle-assisted cell membrane chromatography

Introduction: The Huanglian Jiedu decoction (HLJDD) is a Chinese herbal formula that exerts neuroprotective effects by alleviating oxidative stress injuries and may potentially be prescribed for treating Alzheimer's disease; however, its active ingredients have not yet been identified. Cell membrane chromatography is a high-throughput method for screening active ingredients, but traditional cell membrane chromatography requires multiple centrifugation steps, which affects its separation efficiency. Magnetic nanoparticles are unparalleled in solid-liquid separation and can overcome the shortcomings of traditional cell membrane chromatography. Methods: In this study, the neuroprotective effects of the components of HLJDD were screened through a novel magnetic nanoparticle-assisted cell membrane chromatography method. Magnetic nanoparticles and cell membranes were stably immobilized by amide bonds. Magnetic bead (MB)-immobilized cell membranes of HT-22 cells were incubated with the HLJDD extract to isolate specific binding components. The specific binding components were then identified by ultraperformance liquid chromatography (UPLC)-Orbitrap Fusion Tribrid MS after solid-phase extraction. The bioactivity of these components was analyzed in an HT-22 cellular model of glutamate-induced injury. Results and Discussion: The preparation method of the composite of cell membrane and MBs has the advantages of simple preparation and no introduction of toxic organic reagents. MBs not only provide support for cell membranes, but also greatly improve the separation efficiency compared with traditional cell membrane chromatography. Fifteen of these components were found to specifically bind to the cell membranes, and seven of them were confirmed to reduce varying degrees of glutamate-induced toxicity in HT-22 cells. In conclusion, our findings suggest that the amide bond-based immobilization of magnetic nanoparticles on cell membranes, along with solid-phase extraction and UPLC, is an effective method for isolating and discovering the bioactive components of traditional Chinese medicines.

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Triterpenoid-PEG Ribbons Targeting Selectivity in Pharmacological Effects

(1) Background: To compare the effect of selected triterpenoids with their structurally resembling derivatives, designing of the molecular ribbons was targeted to develop compounds with selectivity in their pharmacological effects. (2) Methods: In the synthetic procedures, Huisgen 1,3-dipolar cycloaddition was applied as a key synthetic step for introducing a 1,2,3-triazole ring as a part of a junction unit in the molecular ribbons. (3) Results: The antimicrobial activity, antiviral activity, and cytotoxicity of the prepared compounds were studied. Most of the molecular ribbons showed antimicrobial activity, especially on Staphylococcus aureus, Pseudomonas aeruginosa, and Enterococcus faecalis, with a 50–90% inhibition effect (c = 25 µg·mL⁻¹). No target compound was effective against HSV-1, but 8a displayed activity against HIV-1 (EC₅₀ = 50.6 ± 7.8 µM). Cytotoxicity was tested on several cancer cell lines, and 6d showed cytotoxicity in the malignant melanoma cancer cell line (G-361; IC₅₀ = 20.0 ± 0.6 µM). Physicochemical characteristics of the prepared compounds were investigated, namely a formation of supramolecular gels and a self-assembly potential in general, with positive results achieved with several target compounds. (4) Conclusions: Several compounds of a series of triterpenoid molecular ribbons showed better pharmacological profiles than the parent compounds and displayed certain selectivity in their effects.

Amide Bond Formation Using 4-Coumarate: CoA Ligase from Arabidopsis thaliana

Amide bond formation is one of the most fundamental reactions in organic chemistry, and amide bonds constitute the key functional groups in natural products, peptides, and pharmaceuticals. Here we demonstrate the chemoenzymatic syntheses of 4-coumaroyl- and hexanoyl-amino acids, using 4-coumarate: CoA ligase from the model plant Arabidopsis thaliana (At4CL2). At4CL2 accepts 4-coumaric acid and hexanoic acid as the carboxylate substrates to generate acyl adenylates, which are captured by the amino group of amino acids to afford a series of N-acyl amides. This study shows the potential of 4CL for application as a biocatalyst to generate a series of biologically active amide compounds.

1,2,3-Triazoles as Biomimetics in Peptide Science

Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.

Chemoselective Amide-Forming Ligation Between Acylsilanes and Hydroxylamines Under Aqueous Conditions

We report the facile amide-forming ligation of acylsilanes with hydroxylamines (ASHA ligation) under aqueous conditions. The ligation is fast, chemoselective, mild, high-yielding and displays excellent functional-group tolerance. Late-stage modifications of an array of marketed drugs, peptides, natural products, and biologically active compounds showcase the robustness and functional-group tolerance of the reaction. The key to the success of the reaction could be the possible formation of the strong Si-O bond via a Brook-type rearrangement. Given its simplicity and efficiency, this ligation has the potential to unfold new applications in the areas of medicinal chemistry and chemical biology.

Amide Synthesis from Thiocarboxylic Acids and Amines by Spontaneous Reaction and Electrosynthesis

Amide bond formation is one of the most important basic reactions in chemistry. A catalyst-free approach for constructing amide bonds from thiocarboxylic acids and amines was developed. The mechanistic studies showed that the disulfide was the key intermediate for this amide synthesis. Thiobenzoic acids could be automatically oxidized to disulfides in air, thioaliphatic acids could be electro-oxidized to disulfides, and the resulting disulfides reacted with amines to give the corresponding amides. By this method, various amides could be easily synthesized in excellent yields without using any catalyst or activator. The successful synthesis of bioactive compounds also highlights the synthetic utility of this strategy in medicinal chemistry.

Chemistry of Bridged Lactams: Recent Developments

Bridged lactams represent the most effective and wide-ranging method of constraining the amide bond in a non-planar conformation. A previous comprehensive review on this topic was published in 2013 (Chem. Rev.2013, 113, 5701–5765). In the present review, which is published as a part of the Special Issue on Amide Bond Activation, we present an overview of the recent developments in the field of bridged lactams that have taken place in the last five years and present a critical assessment of the current status of bridged lactams in synthetic and physical organic chemistry. This review covers the period from 2014 until the end of 2018 and is intended as an update to Chem. Rev.2013, 113, 5701–5765. In addition to bridged lactams, the review covers recent advances in the chemistry of bridged sultams, bridged enamines and related non-planar structures.

Recent Advances in the Addition of Amide/Sulfonamide Bonds to Alkynes

The addition of amide/sulfonamide bonds to alkynes is not only one of the most important strategies for the direct functionalization of carbon⁻carbon triple bonds, but also a powerful tool for the downstream transformations of amides/sulfonamides. The present review provides a comprehensive summary of amide/sulfonamide bond addition to alkynes, including direct and metal-free aminoacylation, based-promoted aminoacylation, transition-metal-catalyzed aminoacylation, organocatalytic aminoacylation and transition-metal-catalyzed aminosulfonylation of alkynes up to December 2018. The reaction conditions, regio- and stereoselectivities, and mechanisms are discussed and summarized in detail.

Structurally Constrained Insulin Analogs by Directed Stepwise Crosslinking

BACKGROUND

Research has been directed at the optimization of insulin for medicinal purposes. An insulin analog that could be reversibly activated might provide more precise pharmacokinetic control and broaden the inherent therapeutic index of the hormone. The prospect of using intramolecular structural constraint to reversibly inactive insulin might constitute the first step to achieving such an optimized analog. Chemically crosslinked insulin analogs have been reported where two amines are covalently linked by reaction with symmetrical bifunctional active esters. There is little selectivity in this synthetic approach to molecular constraint with multiple derivatives being formed.

OBJECTIVE

To systematically evaluate the synthesis of covalently crosslinked insulin analogs by asymmetric methods and the biological consequences.

METHOD

We report synthesis of amine crosslinked insulin analogs via a two-step procedure. The stepwise approach was initiated by amide bond formation and followed by second site alkylation to produce site-specific, cross-linked insulin analogs.

RESULTS

A set of unique insulin analogs crosslinked at the two of the three native amines were synthesized. They were chemical characterized and assessed by in vitro bioanalysis to result in a significant and reasonably consistent reduction in biological potency.

CONCLUSION

We achieved an unambiguous two-step synthesis of several crosslinked insulin analogs differing in location of the chemical tether. Bioanalysis demonstrated the ability of the molecular constraint to reduce bioactivity. The results set the stage for in vivo assessment of whether such a reduction in potency can be used pharmacologically to establish a constrained hormone upon which reversible tethering might be subsequently introduced.

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.

Electronic Effect on the Molecular Motion of Aromatic Amides: Combined Studies Using VT-NMR and Quantum Calculations

Rotational barrier energy studies to date have focused on the amide bond of aromatic compounds from a kinetic perspective using quantum calculations and nuclear magnetic resonance (NMR). These studies provide valuable information, not only regarding the basic conformational properties of amide bonds but also the molecular gear system, which has recently gained interest. Thus, we investigate the precise motion of the amide bonds of two aromatic compounds using an experimental rotational barrier energy estimation by NMR experiments and a theoretical evaluation of the density functional theory calculation. The theoretical potential energy surface scan method combined with the quadratic synchronous transit 3 method and consideration of additional functional group rotation with optimization and frequency calculations support the results of the variable temperature ¹H NMR, with deviations of less than 1 kcal/mol. This detailed experimental and theoretical research strongly supports molecular gear motion in the aromatic amide system, and the difference in kinetic energy indicates that the electronic effect from the aromatic structure has a key role in conformational movements at different temperatures. Our study provides an enhanced basis for future amide structural dynamics research.

An ATP-Dependent Ligase with Substrate Flexibility Involved in Assembly of the Peptidyl Nucleoside Antibiotic Polyoxin

Polyoxin (POL) is an unusual peptidyl nucleoside antibiotic, in which the peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG mutant is capable of accumulating multiple intermediates, including the peptidyl moiety (carbamoylpolyoxamic acid [CPOAA]) and the nucleoside skeletons (POL-C and the previously overlooked thymine POL-C). We further demonstrate that PolG employs an ATP-dependent mechanism for amide bond formation and that the generation of the hybrid nucleoside antibiotic POL-N is also governed by PolG. Finally, we determined that the deduced ATP-binding sites are functionally essential for PolG and that they are highly conserved in a number of related ATP-dependent ligases. These insights have allowed us to propose a catalytic mechanism for the assembly of peptidyl nucleoside antibiotic via an acyl-phosphate intermediate and have opened the way for the combinatorial biosynthesis/pathway engineering of this group of nucleoside antibiotics.IMPORTANCE POL is well known for its remarkable antifungal bioactivities and unusual structural features. Actually, elucidation of the POL assembly logic not only provides the enzymatic basis for further biosynthetic understanding of related peptidyl nucleoside antibiotics but also contributes to the rational generation of more hybrid nucleoside antibiotics via synthetic biology strategy.

Enhanced Cellular Uptake and Pharmacokinetic Characteristics of Doxorubicin-Valine Amide Prodrug

In this study, we synthesized the valine (Val)-conjugated amide prodrug of doxorubicin (DOX) by the formation of amide bonds between DOX and Val. The synthesis of the DOX-Val prodrug was identified by a proton nuclear magnetic resonance (¹H-NMR) assay. In the MCF-7 cells (human breast adenocarcinoma cell; amino acid transporter–positive cell), the cellular accumulation efficiency of DOX-Val was higher than that of DOX according to the flow cytometry analysis data. Using confocal laser scanning microscopy (CLSM) imaging, it was confirmed that DOX-Val as well as DOX was mainly distributed in the nucleus of cancer cells. DOX-Val was intravenously administered to rats at a dose of 4 mg/kg, and the plasma concentrations of DOX-Val (prodrug) and DOX (formed metabolite) were quantitatively determined. Based on the systemic exposure (represented as area under the curve (AUC) values) of DOX-Val (prodrug) and DOX (formed metabolite), approximately half of DOX-Val seemed to be metabolized into DOX. However, it is expected that the remaining DOX-Val may exert improved cellular uptake efficiency in cancer cells after its delivery to the cancer region.

Compounds from the Chinese black ant (Polyrhachis dives) and NMR behavior of the isomers with formamide group

Two new dopamine derivatives divesamides A (1) and B (2), along with six known N-containing compounds were isolated from the Chinese black ant (Polyrhachis dives). Their structures were determined on the basis of spectroscopic methods. Compound 1 is a racemate, and chiral HPLC separation yielded a pair of antipodes. The absolute configuration of (+)-1 was assigned by a computational method. The double signals in the (1)H and (13)C NMR spectra of 2 that resulted from the presence of a formamide group were discussed. The T- and B-lymphocytes proliferation assay showed that 2 has moderate immunosuppressive activity toward T- and B-lymphocytes proliferation at a concentration of 20 μM.

A Continuous Flow System for the Measurement of Ambient Nitrogen Oxides [NO + NO2] Using Rhodamine B Hydrazide as a Chemosensor

A new chemosensor has been used to monitor atmospheric nitrogen oxides [NO + NO₂] at parts per billion (ppb) level. It is based on the catalytic reaction of nitrogen oxides with rhodamine B hydrazide (RBH) to produce a colored compound through the hydrolysis of the amide bond of the molecule. A simple colorimeter has been used to monitor atmospheric nitrogen dioxide at ppb level. The air samples were purged through a sampling cuvette containing RBH solution using peristaltic pump. The proposed method has been successfully applied to monitor the ambient nitrogen dioxide levels at traffic junction points within the city limits and the results obtained are compared with the standard Griess-Ilosvay method.

Amino Acid and Peptide Immobilization on Oxidized Nanocellulose: Spectroscopic Characterization

In this work, oxidized nanocellulose (ONC) was synthesized and chemically coupled with amino acids and peptides using a two step coupling method at room temperature. First, ONC was activated by N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide hydrochloride, forming a stable active ester in the presence of N-hydroxysuccinimide. Second, the active ester was reacted with the amino group of the amino acid or peptide, forming an amide bond between ONC and the grafted molecule. Using this method, the intermolecular interaction of amino acids and peptides was avoided and uniform coupling of these molecules on ONC was achieved. The coupling reaction was very fast in mild conditions and without alteration of the polysaccharide. The coupling products (ONC-amino acids and ONC-peptides) were characterized by transmission electron microscopy and by the absorption, emission, Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) spectroscopic techniques.

Exploring the Backbone of Enkephalins To Adjust Their Pharmacological Profile for the δ-Opioid Receptor

The role of each of the four amide bonds in Leu(5)-enkephalin was investigated by systematically and sequentially replacing each with its corresponding trans-alkene. Six Leu(5)-enkephalin analogs based on six dipeptide surrogates and two Met(5)-enkephalin analogs were synthesized and thoroughly tested using a δ-opioid receptor internalization assay, an ERK1/2 activation assay, and a competition binding assay to evaluate their biological properties. We observed that an E-alkene can efficiently replace the first amide bond of Leu(5)- and Met(5)-enkephalin without significantly affecting biological activity. By contrast, the second amide bond was found to be highly sensitive to the same modification, suggesting that it is involved in biologically essential intra- or intermolecular interactions. Finally, we observed that the affinity and activity of analogs containing an E-alkene at either the third or fourth position were partially reduced, indicating that these amide bonds are less important for these intra- or intermolecular interactions. Overall, our study demonstrates that the systematic and sequential replacement of amide bonds by E-alkene represents an efficient way to explore peptide backbones.