Do polyamines contribute to plant cell wall assembly by forming amide bonds with pectins?

Desorption hysteresis of antibiotics on biochar produced at high temperature: The role of amine groups and amidation reaction

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α‐amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α‐hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α‐hydroxy acids and α‐amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long‐standing hypothesis that peptides might have arisen from ester‐based precursors.

Nonribosomal peptide synthetases (NRPSs) are important enzymes that synthesize an array of nongenetically encoded peptides. The latter have diverse physicochemical properties and roles. NRPSs are modular enzymes in which, for example, the condensation (C-) domain catalyzes the formation of amide bonds. The NRPS tyrocidine synthetase from Brevibacillus brevis is responsible for synthesizing the cyclic-peptide antibiotic tyrocidine. The first step is formation of an amide bond between a proline and phenylalanine which is catalyzed by a C-domain. In this study, a multiscale computational approach (molecular dynamics and QM/MM) has been used to investigate substrate binding and catalytic mechanism of the C-domain of tyrocidine synthetase. Overall, the mechanism is found to proceed through three exergonic steps in which an active site Histidine, His222, acts as a base and acid. First, His222 acts as a base to facilitate nucleophilic attack of the prolyl nitrogen at the phenylalanyl's carbonyl carbon. This is also the rate-limiting step with a free energy barrier of 38.8 kJ mol-1. The second step is collapse of the resulting tetrahedral intermediate with cleavage of the S-C bond between the phenylalanyl and its Ppant arm, along with formation of the above amide bond. Meanwhile, the now protonated His222 imidazole has rotated toward the newly formed thiolate of the Ppant arm. In the final step, His222 acts as an acid, protonating the thiolate and regenerating a neutral His222. The overall mechanism is found to be exergonic with the final product complex being 46.3 kJ mol-1 lower in energy than the initial reactant complex.

A family of covalently linked cell wall proteins of Saccharomyces cerevisiae, called Pir proteins, are characterized by up to 10 conserved repeating units. Ccw5/Pir4p contains only one complete repeating sequence and its deletion caused a release of the protein into the medium. The exchange of each of three glutamines (Gln69, Gln74, Gln76) as well as one aspartic acid (Asp72) within the repeating unit leads to a loss of the protein from the cell wall. Amino acid sequencing revealed that only Gln74 is modified. Release of the protein with mild alkali, changed Gln74 to to glutamic acid, suggesting that Gln74 is involved in the linkage. Analysis by mass spectrometry showed that 5 hexoses are attached to Gln/Glu74. Sugar analysis revealed glucose as the only constituent. It is suggested that Pir proteins form novel, alkali labile ester linkages between the gamma-carboxyl group of glutamic acids, arising from specific glutamines, with hydroxyl groups of glucoses of beta-1,3-glucan chains. This transglutaminase-type reaction could take place extracellularly and would energetically proceed on the account of amido group elimination.

Amide bonds are of central importance for biochemistry; in the guise of peptide bonds, they form the backbone of proteins. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life. Enzyme-free formation of amide bonds between amino acids has been demonstrated in the presence of condensing agents such as cyanamide. Here we report the formation of amide bonds in aqueous solution in the absence of any condensing agent. We find that the formation of pyrite (FeS2) from FeS and H2S can provide the driving force for reductive acetylation of amino acids with mercaptoacetic acid (HSCH2COOH). The redox energy of pyrite formation permits the activation of the carboxylic acid group, which is converted to a species that reacts readily with amines. This process provides support for the chemo-autotrophic theory for the origin of life, in which pyrite formation supplies the energy source for the first autocatalytic reproduction cycle.

Amide bond formation is one of the most important transformations in organic synthesis, drug development, and materials science. Efficient construction of amides has been among the most challenging tasks for organic chemists. Herein, we report a concise methodology for amide bond (-CONH-) formation assisted by vicinal group migration in alkylthio-functionalized enaminones (α-oxo ketene N, S-acetals) under mild conditions. Simple treatment of such enaminones with PhI(OAc)2 at ambient temperature in air afforded diverse multiply functionalized α,β-unsaturated amides including β-cyclopropylated acrylamides, in which a wide array of functional groups such as aryl, (hetero)aryl, alkenyl, and alkyl can be conveniently introduced to a ketene moiety. The reaction mechanism was investigated by exploring the origins of the amide oxygen and carbon atoms as well as isolation and structural characterization of the reaction intermediates. The amide bond formation reactions could also be efficiently performed under solventless mechanical milling conditions.

Peptides and synthetic peptide-like molecules are powerful tools for analysis and control of biological function. One major limitation of peptides is the instability of their interactions with biomolecules, because of the limited accessible surface area for noncovalent interactions and the intrinsic flexibility of peptides. Peptide tags are nonetheless fundamental for protein detection and purification, because their small size minimizes the perturbation to protein function. Here we have designed a 16 amino acid peptide that spontaneously forms an amide bond to a protein partner, via reaction between lysine and asparagine side chains. This depended upon splitting a pilin subunit from a human pathogen, Streptococcus pyogenes, which usually undergoes intramolecular amide bond formation to impart mechanical and proteolytic stability to pili. Reaction of the protein partner was able to proceed to 98% conversion. The amide bond formation was independent of redox state and occurred at pH 5-8. The reaction was efficient in phosphate buffered saline and a wide range of biological buffers. Surprisingly, amide bond formation occurred at a similar rate at 4 and 37 degrees C. Both peptide and protein partners are composed of the regular 20 amino acids and reconstituted efficiently inside living E. coli. Labeling also showed high specificity on the surface of mammalian cells. Irreversible targeting of a peptide tag may have application in bioassembly, in cellular imaging, and to lock together proteins subject to high biological forces.

Amide bonds are ubiquitous in peptides, proteins, pharmaceuticals, and polymers. The formation of amide bonds is a straightforward process: amide bonds can be synthesized with relative ease because of the availability of efficient coupling agents. However, there is a substantive need for methods that do not require excess reagents. A catalyst that condenses amino acids could have an important impact by reducing the significant waste generated during peptide synthesis. We describe the rational design of a biomimetic catalyst that can efficiently couple amino acids featuring standard protecting groups. The catalyst design combines lessons learned from enzymes, peptide biosynthesis, and organocatalysts. Under optimized conditions, 5 mol % catalyst efficiently couples Fmoc amino acids without notable racemization. Importantly, we demonstrate that the catalyst is functional for the synthesis of oligopeptides on solid phase. This result is significant because it illustrates the potential of the catalyst to function on a substrate with a multitude of amide bonds, which may be expected to inhibit a hydrogen-bonding catalyst.

Amidation and esterification of carboxylic acids with amines and phenols by N,N′-diisopropylcarbodiimide: A new approach for amide and ester bond formation in water

1. Rumen bacteria were prepared in bulk from freshly killed sheep. They were exposed to ultrasonic disintegration and a preparation of cell walls was made by differential centrifugation.2. The amino acid composition of acid hydrolysates of whole cells and cell walls was determined. Summation of these results shows that whole cells contained approximately 40% amino acids and cell walls approximately 30%.3. A considerable proportion of the alanine content of cell walls was present as the D-isomer, partly ester linked as in teichoic acids and partly more tightly bound in ‘peptide linkage’ being released only after hydrolysis in constant boiling hydrochloric acid.4. Cell walls were found to possess an alanine racemase which was inactivated only after incubation of the cell walls in 0.1 M-NaOH.5. Whole cells contained approximately 8% carbohydrates and cell walls approximately 5%. The glucose and galactose contents of whole cells and cell walls were low, accounting for little more than 2% of the dry weight of the bacterial samples.6. The amino sugar content of bacterial samples was approximately 3% and consisted mainly of glucosamine.7. The total lipid content of rumen bacteria was approximately 25% and that of cell walls varied considerably between 10 and 23%.

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne disease in cattle and other ruminants, is proposed to be at least one of the causes of Crohn disease in humans. MAP and Mycobacterium avium subspecies avium, a closely related opportunistic environmental bacterium, share 95% of their genes and exhibit homologies of more than 99% between these genes. The identification of molecules specific for MAP is essential for understanding its pathogenicity and for development of useful diagnostic tools. The application of gas chromatography, mass spectrometry, and nuclear magnetic resonance led to the structural identification of a major cell wall lipopeptide of MAP, termed Para-LP-01, defined as C20 fatty acyl-D-Phe-N-Me-L-Val-L-Ile-L-Phe-L-Ala methyl ester. Variations of this lipopeptide with different fatty acyl moieties (C16 fatty acyl through C17, C18, C19, C21 to C22) were also identified. Besides the specificity of this lipopeptide for MAP, the presence of an N-Me-L-valine represents the first reported N-methylated amino acid within an immunogenic lipopeptide of mycobacteria. Sera from animals with Johne disease, but not sera from uninfected cattle, reacted with this lipopeptide, indicating potential biological importance.

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.

Amide bond construction has garnered significant interest in recent decades due to amides being one of the most prevalent functional groups among bioactive molecules. Out of the thirty‐seven new drugs approved by the FDA in 2022, eleven are small molecules containing at least one amide bond. Additionally, there are nineteen large molecules approved as new drugs, some of which have peptide structures, and therefore, also bear amide bonds. In recent years, multiple teams have embraced the challenge of developing more efficient methods for amide bond formation. This dedication has led to numerous publications appearing monthly in prestigious journals, showcasing significant advancements in this field. The primary goal of this review is to present the most viable strategies for constructing the amide bond. It is crucial to differentiate between amide bond formation and amide synthesis; hence, the focus is on describing specific methods for forming new C(O)−N bonds. In particular, this review concentrates on the methods developed within the last six years. There is a particular emphasis on new approaches that consider the thought process when selecting the starting materials and functional groups. This approach ensures coverage of all the most common chemical transformations that yield new amide bonds.

The synthesis of a series of 6‐spiro‐1,4‐diazepane‐2,5‐diones containing an arylpropylamide moiety via head‐to‐tail cyclisation of a terminal amine and a terminal carboxylate ester is described. To induce ring closure of the dipeptide precursor, both lactamisation of the N4/C5 amide bond and N1/C2 amide bond were investigated. Whereas ring closure of the N4/C5 amide bond proved unsuccessful, ring closure of the N1/C2 amide bond was more viable. Furthermore, it was discovered that incorporation of a N,N‐disubstituted amide bond in the peptide sequence was essential for cyclisation to occur. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)