Peptide Bond Research Articles

Role of the initiation factor 3 in the fidelity of initiator tRNA selection on ribosome.

Initiation factors play critical roles in fine-tuning translation initiation, which is the first and the rate-limiting step in protein synthesis. In bacteria, initiation factors, IF1, IF2 and IF3 work in concert to accurately position the initiator tRNA (i-tRNA) in its formyl-aminoacyl form, and the mRNA start codon at the ribosomal P-site, setting the stage for accommodation of the aminoacyl-tRNA in response to the second codon, and formation of the first peptide bond. Among these, IF3 is particularly crucial in ensuring the fidelity of translation initiation as it is involved in the accuracy of the selection of i-tRNA and the start codon. The two-domains (N- and C-terminal) dumbbell shaped structure and dynamics of IF3 significantly influence its fidelity function. This review explores how the N- and C-terminal domains of IF3 communicate with each other and how their interaction with i-tRNA helps to maintain the fidelity of translation initiation.

Role of chirality in photoinduced electron transfer in pentapeptide (L)-His-(L/D)-Asp-(L/D)-Ser-Gly-(L)Tyr in solutions

Factors governing electron transfer (ET) in proteins and peptides are widely studied due to the role of ET in biologically important processes. One of them is the influence of the optical configuration of amino acids on the ability of peptides to aggregate into ensembles: dimers, oligomers, fibrils. Such assemblies, called amyloids, are known to contain D-isomers of asparagine and serine, and their presence in aging living organisms leads to a number of diseases, including Alzheimer’s disease. However, how these amino acids affect the structure and properties of peptides have not yet been established. Using the example of the pentapeptide (PP)-(L)histidine-(L)asparagine-(L)serine-glycine-(L)tyrosine and its analogues with D-asparagine and D-serine, this article studies the comparative reactivity of optical isomers in photoinduced ET using chemically induced dynamic nuclear polarization (CIDNP), fluorescence spectroscopy and quantum chemical calculations. The CIDNP method was chosen because it had previously demonstrated high sensitivity to ET processes in chiral dyads linked by non-covalent interactions. ET involving Tyr and His residues of PP was detected under UV irradiation both in the presence of an electron acceptor, naproxen, and during photolysis of PP itself. It was shown that the efficiency of ET and PP fluorescence quenching differ for optical isomers of asparagine and serine. In addition, the dependence of the CIDNP efficiency on the PP concentration showed that ET between Tyr and peptide bonds can occur in the dimer of the PP. Quantum chemical calculation confirm the possibility of PP self-association.

γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells.

Connecting two small molecules, such as ligands, fluorophores, or lipids, together via a linker with amide bonds is a widely used strategy to generate synthetic bifunctional molecules for various biological and biomedical applications. Such bifunctional molecules have been used in live-cell experiments under the assumption that they should be stable in cells. However, we recently found that a membrane-targeting bifunctional molecule, composed of a lipopeptide and the small-molecule ligand trimethoprim, referred to as mgcTMP, underwent amide-bond cleavage in mammalian cells. In this work, we first identified γ-secretase as the major protease degrading mgcTMP in cells. We next investigated the intracellular degradation of several different types of amide-linked bifunctional compounds and found that N-terminally fatty acid-conjugated small molecules are susceptible to γ-secretase-mediated amide-bond cleavage. In contrast, amide-linked bifunctional molecules composed of two small molecules, such as ligands and hydrophobic groups, which lack lipid modification, did not undergo intracellular degradation. These findings highlight a previously overlooked consideration for the development and application of lipid-based bifunctional molecules in chemical biology research.

Development of the Esterase PestE for Amide Bond Synthesis Under Aqueous Conditions: Enzyme Cascades for Converting Waste PET into Tamibarotene

AbstractA growing number of hydrolase enzymes show promiscuous acyltransferase activity, even under aqueous conditions. Here we report, for the first time, the ability of Pyrobaculum calidifontis VA1 esterase (PestE) to catalyse the formation of a wide range of amides in buffer, where the acyl donor forms a significant structural component in the amide product. The reactions occur under mild conditions and can achieve conversions up to 97 % in 6 h for formation of N‐benzylfuranamide as the model reaction. We demonstrate PestE's potential in enzyme cascades to make amides from waste PET plastic and the conversion of the terephthalic acid product to tamibarotene, a drug with activity against acute leukemia. Rational mutagenesis led to identification of PestE variants F33L F289A and F33L. F33L F289A increased conversion of N‐benzylfuranamide by 1.2‐fold, and F33L gave a 4‐fold increase in conversion to tamibarotene.

Development of the Esterase PestE for Amide Bond Synthesis Under Aqueous Conditions: Enzyme Cascades for Converting Waste PET into Tamibarotene.

A growing number of hydrolase enzymes show promiscuous acyltransferase activity, even under aqueous conditions. Here we report, for the first time, the ability of Pyrobaculum calidifontis VA1 esterase (PestE) to catalyse the formation of a wide range of amides in buffer, where the acyl donor forms a significant structural component in the amide product. The reactions occur under mild conditions and can achieve conversions up to 97 % in 6 h for formation of N-benzylfuranamide as the model reaction. We demonstrate PestE's potential in enzyme cascades to make amides from waste PET plastic and the conversion of the terephthalic acid product to tamibarotene, a drug with activity against acute leukemia. Rational mutagenesis led to identification of PestE variants F33L F289A and F33L. F33L F289A increased conversion of N-benzylfuranamide by 1.2-fold, and F33L gave a 4-fold increase in conversion to tamibarotene.

Input Pose is Key to Performance of Free Energy Perturbation: Benchmarking with Monoacylglycerol Lipase.

Free energy perturbation (FEP) methodologies have become commonplace methods for modeling potency in hit-to-lead and lead optimization stages of drug discovery. The conformational states of the initial poses of compounds for FEP+ calculations are often set up by alignment to a cocrystal structure ligand, but it is not clear if this method provides the best result for all proteins or all ligands. Not only are ligand conformational states potential variables in modeling compound potency in FEP but also the selection of crystallographic water molecules for inclusion in the FEP input structures can impact FEP models. Here, we report the results of FEP calculations using FEP+ from Schrödinger and starting from maximum common substructure alignment and docked poses generated with an array of docking methodologies. As a benchmark data set, we use monoacylglycerol lipase (MAGL), an important clinical drug target in cancer malignancy, neurological diseases, and metabolic disorders, and a set of 17 MAGL inhibitors. We found a large variation among FEP+ correlations to experimental IC50 values depending on the method used to generate the input pose and that the inclusion of ligand-based information in the docking process, with some methods, increases the correlation between FEP+ free energies and IC50 values. Upon analysis of the initial poses, we found that the differences in FEP+ correlations stemmed from rotation around a tertiary amide bond as well as translation of the compound toward the more hydrophobic side of the MAGL pocket. FEP+ estimation improved across all pose modeling methods when hydrogen bond constraint information was added. However, simple maximum common substructure alignment in the presence of all crystallographic water molecules outperformed all other methods in correlation between estimated and experimental IC50 values. Taken together, these findings suggest that pose selection and crystallographic water inclusion greatly impact how well FEP+ estimated IC50 values align with experimental IC50 values and that modelers should benchmark a few different pose generation methodologies and different water inclusion strategies for their hit-to-lead and lead optimization drug discovery projects.

Natural serine proteases and their applications in combating amyloid formation

Background and purpose: Amyloidosis is a group of diseases including diabetes type II and neurological disorders, such as Alzheimer’s disease, Parkinson’s disease, prion disease, etc., where a common trait is observed; accumulation of misfolded protein at different parts of the body, especially the brain which manifests the typical symptoms like dementia, movement disorders, etc. These misfolded proteins, named amyloids, are protease resistant and thus it becomes difficult to manage these diseases in vivo. Enzymes that catalyse the complete breakdown of proteins are known as proteases. The peptide bonds in proteins are degraded by these serine proteases, which cause amyloid disaggregation. Experimental approach: We have searched for related articles using the search engines Google Scholar, PubMed, and Scopus for the past 10 years, selected the relevant articles, and written the outcomes and benefits of protease using the medical topic “serine protease” and the following text phrases -keratinase, lumbrokinase, serratiopeptidase, nattokinase. Key results: Alkaline serine proteases exhibit activity within the neutral to alkaline pH range. They are most capable of degrading host complement proteins, cytokines, and host clotting factors mostly due to their serine centre or metallotype. Because of its potential usage in food, pharmaceutical, and other industrial domains, this category of enzymes has been extensively investigated. Specifically, serine proteases are a group of enzymes that can be consumed orally and are stable in our gastrointestinal tract. Conclusion: In this review, we discussed the role of different serine proteases in amyloid aggregate inhibition and their potential application in treating amyloidosis.

Synthesis of new bis(pyrazolo[1,5-a]pyrimidines) linked to different spacers with potential MurB inhibitory activity utilizing 1H-pyrazole-3,5-diamines

Recently, there has been an increased interest in developing new antibacterial agents that target the MurB inhibition, which is necessary for bacterial survival. We developed a two-step tandem protocol to synthesize 15 new bis(pyrazolo[1,5-a]pyrimidines), which are attached to alkane cores by amide linkages. The protocol involved reacting the appropriate bis(2-cyanoacetamides) with dimethylformamide-dimethylacetal in toluene at 80 °C for 3-4 h. The crude bis(2-cyano-3-(dimethylamino)acrylamides) was collected, then reacted with 3,5-diamino-1H-pyrazoles. The reaction gave the desired products in 82-92% yields after 5-6 h of heating at reflux in pyridine. Bis(2,7-diamino-3-(4-methoxybenzyl)pyrazolo[1,5-a]pyrimidine-6-carboxamides) demonstrated comparable efficacy to ciprofloxacin. Their MIC and MBC ranged from 2.8-3.0 and 5.7-6.0 µM, respectively, against S. aureus and E. coli. Moreover, these products displayed promising MurB inhibitory activity with IC50 ranging from 7.8 to 8.0 µM.

Comprehensive Overview of the Amide Linker Modification in the Succinate Dehydrogenase Inhibitors.

Succinate dehydrogenase inhibitors (SDHIs) have become one of the most important classes of agrochemical fungicides. According to the data from FRAC, the resistance risk for SDHIs had reached up to medium and even to high. In general, the chemical structure of SDHIs mainly contained three fragments: an acid core, a hydrophobic tail, and an amide linker, corresponding to three modification directions for each fragment. Among them, amide linker modification (ALM) has become a research hotspot for the design of novel SDHIs fungicides in recent years. We presented here a detailed review on the ALM strategy in the past decade, and some of them had entered the market. According to their chemical structures, ALM strategy were classified into four parts: (1) linked aliphatic chain between amide bond and hydrophobic tail, (2) introducing substituents to replacing hydrogen atom in the amide bond, (3) reverse extending the amide linker, and (4) changed with other bioisosteres. Moreover, the structure-activity relationship and the interaction mechanism of ALM-SDHI with SDH were discussed. This review aims to provide a global perspective on research and development of novel SDHIs, as well as suggestions for food safety management.

Insights into Chemical Bonding Modes and Heat Transport at the Molecular Level.

Despite the demand for nanoscale thermal management technologies of material surfaces and interfaces using organic molecules, heat transport properties at the single molecular level remain elusive due to the experimental difficulty of measuring temperature at the nanoscopic scale. Here we show how chemical bonding modes can affect the heat transport properties of single molecules. We focused on four molecular systems: benzylthiol linked to another phenyl group by either a triple (compound 1), double (3), or amide (4) bond and a common linear alkanethiol (2), all of which are nearly identical in molecular length. We prepared binary self-assembled monolayers (SAMs) using 1 as a common reference in combination with 2-4 and investigated their relative heat transport properties using scanning thermal microscopy (SThM). Two-dimensional temperature mapping of the binary SAMs showed that C≡C and C=C bonds provide more effective pathways for heat transport compared to C-C bonds. Since the amide molecule has resonance structures with C=N double bond character, we expected that its heat transport properties would be comparable to those of the thiols containing triple or double bonds. However, the heat transport properties of this molecule prevailed over the others, most likely due to the formation of additional heat transport pathways caused by intermolecular hydrogen bonding. These findings may provide important guidelines for the design of organic materials for nanoscale thermal management.

DeepBBQ: A Deep Learning Approach to the Protein Backbone Reconstruction.

Coarse-grained models have provided researchers with greatly improved computational efficiency in modeling structures and dynamics of biomacromolecules, but, to be practically useful, they need fast and accurate conversion methods back to the all-atom representation. Reconstruction of atomic details may also be required in the case of some experimental methods, like electron microscopy, which may provide Cα-only structures. In this contribution, we present a new method for recovery of all backbone atom positions from just the Cα coordinates. Our approach, called deepBBQ, uses a deep convolutional neural network to predict a single internal coordinate per peptide plate, based on Cα trace geometric features, and then proceeds to recalculate the cartesian coordinates based on the assumption that the peptide plate atoms lie in the same plane. Extensive comparison with similar programs shows that our solution is accurate and cost-efficient. The deepBBQ program is available as part of the open-source bioinformatics toolkit Bioshell and is free for download and the documentation is available online.

Bioinspired peptide sensors with tailorable structure for specific and in-situ tracking of Hg2+ biodistribution in living cells upon acute exposure

Metal-biomolecule interactions that are ubiquitous in nature provide fundamental knowledge and rich structural motifs for the development of functional molecules and smart sensors. In this work, inspired by the active sites in metalloproteins, a biomimetic peptide sensor was designed for the selective recognition and activatable sensing of Hg2+ in living biosystems. Tetraphenylethylene (TPE) with typical aggregation-induced emission (AIE) behavior, was introduced as the activatable signal transducer to enable high signal-to-background signaling. The tailorable side chains and flexible peptide linkage were exploited to tune the coordination affinity, selectivity, and fluorescence response toward Hg2+. Benefiting from the rapid response (1 min), high specificity and nanomolar sensitivity, the peptide sensor allows investigating the mechanism of acute toxicity of Hg2+. Capable of penetrating plasma membrane, the peptide sensor revealed the dosage-dependent and dynamic subcellular biodistribution behavior of Hg2+. The finding that Hg2+ preferentially accumulates and rapidly enriches in nucleoli of cells upon short exposure, evidences the adverse effect toward ribosome biogenesis and the resultant genetic deficiencies. These results highlight the peptide sensors as promising tools for not only on-site detection, but also studying the cell biology and toxicology of this metal ion in living biosystems.

Macromorphological characterization of filamentous fungi isolated from ripened cheese samples as potential protease producers

Proteases catalyze the hydrolysis of amide bonds of peptides and proteins, thereby playing crucial roles in the functioning of organisms, as well as having an important role in industrial processes. They are one of the three most widely commercially marketed enzymes. This study aimed to analyze the macromorphological characteristics of seventeen filamentous fungi and identify potential protease producers. The microorganisms were cultivated on a solid culture medium containing skim milk powder at 30 °C for seven days. After the incubation period, macroscopic morphological characteristics of the fungi were observed, and the strain diameters and the enzymatic halos around the colonies were measured. As a result, a wide variety of characteristics among the filamentous fungi was observed, highlighting the diversity of this group. Additionally, Potentials asprotease producers under the conditions presented were observed for eight filamentous fungi. These findings suggest that the these fungal strains might be valuable resources for the production of proteases with high biotechnological potentials.

De(sulfon)amidative Cyclization: The Synthesis of Dibenzolactams and Dibenzosultams for Organic Light Emitting Diode Materials

AbstractThis study addresses a challenge in organic synthetic chemistry: the direct cleavage of amide bonds, which is typically hampered by the thermodynamic stability of the C(Ar)−C(acyl) bond. Previous methods often rely on “CO” extrusion‐jointing transition metal‐catalyzed process and require activated tertiary amides, limiting their applicability due to incompatibility with reactive functional groups such as halogens. Herein, we report a transition metal‐free approach for the deamidative cyclization of biaryl diamides via a radical process, yielding dibenzolactam derivatives. Along this line, we have developed the desulfonamidative cyclization of biaryl disulfonamides to produce dibenzosultams through direct nucleophilic aromatic substitution, demonstrating high selectivity for unsymmetrical structures. Additionally, unsymmetrical sulfamoyl biaryl amides, containing both amide and sulfonamide functionalities, can selectively undergo desulfonamidative coupling with the amide to form dibenzolactams, which offers a complementary synthetic pathway to unsymmetric dibenzolactams. These protocols exhibit excellent compatibility with reactive functional groups, including halogens, providing an innovative synthetic toolbox for the development of thermally activated delayed fluorescence (TADF) materials used in organic light emitting diodes (OLEDs). DMAC‐PDO, incorporating a dibenzolactam as the acceptor unit, serves as an efficient blue TADF emitter with a maximum external quantum efficiency (EQEmax) of 23.4 %.

De(sulfon)amidative Cyclization: The Synthesis of Dibenzolactams and Dibenzosultams for Organic Light Emitting Diode Materials.

This study addresses a challenge in organic synthetic chemistry: the direct cleavage of amide bonds, which is typically hampered by the thermodynamic stability of the C(Ar)-C(acyl) bond. Previous methods often rely on "CO" extrusion-jointing transition metal-catalyzed process and require activated tertiary amides, limiting their applicability due to incompatibility with reactive functional groups such as halogens. Herein, we report a transition metal-free approach for the deamidative cyclization of biaryl diamides via a radical process, yielding dibenzolactam derivatives. Along this line, we have developed the desulfonamidative cyclization of biaryl disulfonamides to produce dibenzosultams through direct nucleophilic aromatic substitution, demonstrating high selectivity for unsymmetrical structures. Additionally, unsymmetrical sulfamoyl biaryl amides, containing both amide and sulfonamide functionalities, can selectively undergo desulfonamidative coupling with the amide to form dibenzolactams, which offers a complementary synthetic pathway to unsymmetric dibenzolactams. These protocols exhibit excellent compatibility with reactive functional groups, including halogens, providing an innovative synthetic toolbox for the development of thermally activated delayed fluorescence (TADF) materials used in organic light emitting diodes (OLEDs). DMAC-PDO, incorporating a dibenzolactam as the acceptor unit, serves as an efficient blue TADF emitter with a maximum external quantum efficiency (EQEmax) of 23.4 %.

Photochemical Deracemization of N‐Carboxyanhydrides En Route to Chiral α‐Amino Acid Derivatives

AbstractReadily accessible, racemic N‐carboxyanhydrides (NCAs) of α‐amino acids underwent a deracemization reaction upon irradiation at λ=366 nm in the presence of a chiral benzophenone catalyst. The enantioenriched NCAs (up to 98 % ee) serve as activated α‐amino acid surrogates and, due to their instability, they were directly converted into consecutive products. N‐Protected α‐amino acid esters were obtained after reaction with MeOH and N‐benzoylation (14 examples, 70 %‐quant., 82–96 % ee). Other consecutive reactions included amide (ten examples, 65 %‐quant., 90–98 % ee) and peptide (three examples, 75–89 %, d. r.=97/3 to 94/6) bond formation. Limitations of the method relate for some NCAs to issues with solubility, photooxidation, and high configurational lability.

Photochemical Deracemization of N-Carboxyanhydrides En Route to Chiral α-Amino Acid Derivatives.

Readily accessible, racemic N-carboxyanhydrides (NCAs) of α-amino acids underwent a deracemization reaction upon irradiation at λ=366 nm in the presence of a chiral benzophenone catalyst. The enantioenriched NCAs (up to 98 % ee) serve as activated α-amino acid surrogates and, due to their instability, they were directly converted into consecutive products. N-Protected α-amino acid esters were obtained after reaction with MeOH and N-benzoylation (14 examples, 70 %-quant., 82-96 % ee). Other consecutive reactions included amide (ten examples, 65 %-quant., 90-98 % ee) and peptide (three examples, 75-89 %, d. r.=97/3 to 94/6) bond formation. Limitations of the method relate for some NCAs to issues with solubility, photooxidation, and high configurational lability.

Site‐Selective Construction of N‐Linked Glycopeptides through Photoredox Catalysis

AbstractThe glycosylation of peptides and proteins can significantly impact their intrinsic properties, such as conformation, stability, antigenicity, and immunogenicity. Current methods for preparing N‐linked glycopeptides typically rely on amide bond formation, which can be limited by the presence of reactive functional groups like acids and amines. Late‐stage functionalization of peptides offers a promising approach to obtaining N‐linked glycopeptides. In this study, we demonstrate the preparation of N‐linked glycopeptides through a photoredox‐catalyzed site‐selective Giese addition between N‐glycosyl oxamic acid and peptides containing dehydroalanine (Dha) under visible light conditions. Unlike traditional methods that rely on the coupling of aspartic acid and glycosylamine, this approach utilizes the conjugation of N‐glycosylated carbamoyl radicals with Dha, facilitating the straightforward modification of complex peptides.

Upcycling of Polyamide Wastes to Tertiary Amines Using Mo Single Atoms and Rh Nanoparticles.

The pursuit of sustainable practices through the chemical recycling of polyamide wastes holds significant potential, particularly in enabling the recovery of a range of nitrogen-containing compounds. Herein, we report a novel strategy to upcycle polyamide wastes to tertiary amines with the assistance of H2 in acetic acid under mild conditions (e.g., 180 °C), which is achieved over anatase TiO2 supported Mo single atoms and Rh nanoparticles. In this protocol, the polyamide is first converted into diacetamide intermediates via acidolysis, which are subsequently hydrogenated into corresponding carboxylic acid monomers and tertiary amines in 100 % selectivity. It is verified that Mo single atoms and Rh nanoparticles work together to activate both amide bonds of the diacetamide intermediate, and synergistically catalyze its hydrodeoxygenation to form tertiary amine, but this catalyst is ineffective for hydrogenation of carboxylic acid. This work presents an effective way to reconstruct various polyamide wastes into tertiary amines and carboxylic acids, which may have promising application potential.

Upcycling of Polyamide Wastes to Tertiary Amines Using Mo Single Atoms and Rh Nanoparticles

AbstractThe pursuit of sustainable practices through the chemical recycling of polyamide wastes holds significant potential, particularly in enabling the recovery of a range of nitrogen‐containing compounds. Herein, we report a novel strategy to upcycle polyamide wastes to tertiary amines with the assistance of H2 in acetic acid under mild conditions (e.g., 180 °C), which is achieved over anatase TiO2 supported Mo single atoms and Rh nanoparticles. In this protocol, the polyamide is first converted into diacetamide intermediates via acidolysis, which are subsequently hydrogenated into corresponding carboxylic acid monomers and tertiary amines in 100 % selectivity. It is verified that Mo single atoms and Rh nanoparticles work together to activate both amide bonds of the diacetamide intermediate, and synergistically catalyze its hydrodeoxygenation to form tertiary amine, but this catalyst is ineffective for hydrogenation of carboxylic acid. This work presents an effective way to reconstruct various polyamide wastes into tertiary amines and carboxylic acids, which may have promising application potential.