Natural Amino Acids Research Articles

Design, synthesis and bioactivity evaluation of novel monomethyl auristatin F analogues.

Monomethyl auristatin F (MMAF), a synthetic analogue of the natural compound dolastatin 10, has garnered significant attention in cancer research due to its high potency in vitro. While previous studies have focused on modifying the N-terminal extension of the amino group and the C-terminal modification of the carboxyl group, there has been limited exploration into modifying the P1 and P5 side chains. In this study, we substituted the valine residue at the P1 position with various natural or unnatural amino acids and introduced triazole functional groups at the P5 side chain. Compounds 11k and 18d exhibited excellent inhibition on tubulin. Additionally, compound 18d demonstrated enhanced cytotoxicity against HCT116 cells compared to the parent compound MMAF, suggesting its potential as a cytotoxic payload for further antibody-drug conjugates (ADCs) development.

The Intra- and Intermolecular Friedel-Crafts Acylation of Amino Acid Derivatives in Stereo-Retarded Manner

Abstract: The Friedel-Crafts acylation of natural or unnatural amino acids in stereo-retarded manner is willing to prescribed here. Depending on its main skeleton, the typical intra- and intermolecular Friedel-Crafts reaction of amino acids can be differentiated. The unique amino acid’s general structure can contribute to the reaction between its carboxyl group and the side chain. Depending on the Friedel-Crafts reaction condition, the amino acid’s optical retention can be retarded. This perspective can contribute to the development of this one-century reaction in the field of organic chemistry.

Fluorinated tags to study protein conformation and interactions using19F NMR.

The incorporation of fluorine atoms into a biomacromolecule provides a background-free and environmentally sensitive reporter of structure, conformation and interactions using19F NMR. There are several methods to introduce the19F reporter - either by synthetic incorporationviasolid phase peptide synthesis; by suppressing the incorporation or biosynthesis of a natural amino acid and supplementing the growth media with a fluorinated counterpart during protein expression; and by genetic code expansion to add new amino acids to the amino acid alphabet. This review aims to discuss progress in the field of introducing fluorinated handles into biomolecules for NMR studies by post-translational bioconjugation or 'fluorine-tagging'. We will discuss the range of chemical tagging 'warheads' that have been used, explore the applications of fluorine tags, discuss ways to enhance reporter sensitivity and how the signal to noiseratioscan be boosted. Finally, we consider some key challenges of the field and offer some ideas for future directions.

Optimization of quenched fluorescent peptide substrates of SARS-CoV-2 3CLpro main protease (Mpro) from proteomic identification of P6-P6' active site specificity.

SARS-CoV-2 3C-like main protease (3CLpro) is essential for protein excision from the viral polyprotein. 3CLpro inhibitor drug development to block SARS-CoV-2 replication focuses on the catalytic non-prime (P) side for specificity and potency, but the importance of the prime (P') side in substrate specificity and for drug development remains underappreciated. We determined the P6-P6' specificity for 3CLpro from >800 cleavage sites that we identified using Proteomic Identification of Cleavage site Specificity (PICS). Cleavage occurred after the canonical P1-Gln and non-canonical P1-His and P1-Met residues. Moreover, P3 showed a preference for Arg/Lys and P3' for His. Essential H-bonds between the N-terminal Ser1 of protomer-B in 3CLpro dimers form with P1-His, but not with P1-Met. Nonetheless, cleavage occurs at P1-Met456 in native MAP4K5. Elevated reactive oxygen species in SARS-CoV-2 infection oxidize methionines. Molecular simulations revealed P1-MetOX forms an H-bond with Ser1 and notably, strong positive cooperativity between P1-Met with P3'-His was revealed, which enhanced peptide-cleavage rates. The highly plastic S3' subsite accommodates P3'-His that displays stabilizing backbone H-bonds with Thr25 lying central in a "'threonine trio" (Thr24-Thr25-Thr26) in the P'-binding domain I. Molecular docking simulations unveiled structure-activity relationships impacting 3CLpro-substrate interactions, and the role of these structural determinants was confirmed by MALDI-TOF-MS cleavage assays of P1'- and P3'-positional scanning peptide libraries carrying a 2nd optimal cut-site as an internal positive control. These data informed the design of two new and highly soluble 3CLproquenched-fluorescent peptide substrates for improved FRET monitoring of 3CLpro activity with 15× improved sensitivity over current assays.IMPORTANCEFrom global proteomics identification of >800 cleavage sites, we characterized the P6-P6' active site specificity of SARS-CoV-2 3CLpro using proteome-derived peptide library screens, molecular modeling simulations, and focussed positional peptide libraries. In P1', we show that alanine and serine are cleaved 3× faster than glycine and the hydrophobic small amino acids Leu, Ile, or Val prevent cleavage of otherwise optimal non-prime sequences. In characterizing non-canonical non-prime P1 specificity, we explored the unusual P1-Met specificity, discovering enhanced cleavage when in the oxidized state (P1-MetOX). We unveiled unexpected amino acid cooperativity at P1-Met with P3'-His and noncanonical P1-His with P2-Phe, and the importance of the threonine trio (Thr24-Thr25-Thr26) in the prime side binding domain I in defining prime side binding in SARS-CoV-2 3CLpro. From these analyses, we rationally designed quenched-fluorescence natural amino acid peptide substrates with >15× improved sensitivity and high peptide solubility, facilitating handling and application for screening of new antiviral drugs.

Engineered Phenylalanine Ammonia‐Lyases for the Enantioselective Synthesis of Aspartic Acid Derivatives

Biocatalytic hydroamination of alkenes is an efficient and selective method to synthesize natural and unnatural amino acids. Phenylalanine ammonia‐lyases (PALs) have been previously engineered to access a range of substituted phenylalanines and heteroarylalanines, but their substrate scope remains limited, typically including only arylacrylic acids. Moreover, the enantioselectivity in the hydroamination of electron‐deficient substrates is often poor. Here, we report the structure‐based engineering of PAL from Planctomycesbrasiliensis (PbPAL), enabling preparative‐scale enantioselective hydroaminations of previously inaccessible yet synthetically useful substrates, such as amide‐ and ester‐containing fumaric acid derivatives. Through the elucidation of cryo‐electron microscopy (cryo‐EM) PbPAL structure and screening of the structure‐based mutagenesis library, we identified the key active site residue L205 as pivotal for dramatically enhancing the enantioselectivity of hydroamination reactions involving electron‐deficient substrates. Our engineered PALs demonstrated exclusive a‐regioselectivity, high enantioselectivity, and broad substrate scope. The potential utility of the developed biocatalysts was further demonstrated by a preparative‐scale hydroamination yielding tert‐butyl protected l‐aspartic acid, widely used as intermediate in peptide solid‐phase synthesis.

Engineered Phenylalanine Ammonia-Lyases for the Enantioselective Synthesis of Aspartic Acid Derivatives.

Biocatalytic hydroamination of alkenes is an efficient and selective method to synthesize natural and unnatural amino acids. Phenylalanine ammonia-lyases (PALs) have been previously engineered to access a range of substituted phenylalanines and heteroarylalanines, but their substrate scope remains limited, typically including only arylacrylic acids. Moreover, the enantioselectivity in the hydroamination of electron-deficient substrates is often poor. Here, we report the structure-based engineering of PAL from Planctomycesbrasiliensis (PbPAL), enabling preparative-scale enantioselective hydroaminations of previously inaccessible yet synthetically useful substrates, such as amide- and ester-containing fumaric acid derivatives. Through the elucidation of cryo-electron microscopy (cryo-EM) PbPAL structure and screening of the structure-based mutagenesis library, we identified the key active site residue L205 as pivotal for dramatically enhancing the enantioselectivity of hydroamination reactions involving electron-deficient substrates. Our engineered PALs demonstrated exclusive a-regioselectivity, high enantioselectivity, and broad substrate scope. The potential utility of the developed biocatalysts was further demonstrated by a preparative-scale hydroamination yielding tert-butyl protected l-aspartic acid, widely used as intermediate in peptide solid-phase synthesis.

Genetic code expansion, an emerging tool in the Ca2+ ion channel field.

Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.

Cryogenic gastronomy at The Restaurant at the End of the Universe – exploring interstellar serine synthesis from α-glycyl radical and other ingredients

Amino acids are essential for Earth-like life and are hypothesised to have originated in interstellar space, potentially being transported to Earth via meteorite impacts. Detecting amino acids in interstellar environments and understanding their formation mechanisms through laboratory experiments are crucial for supporting this hypothesis and unravelling the origins of life. In this study, the formation of serine ( NH 2 CH ( CH 2 OH ) COOH ) from α-glycyl ( NH 2 C ⋅ HCOOH ) and hydroxymethyl ( ⋅ CH 2 OH ) radicals was investigated using quantum chemical computations. It was found that the anticipated recombination reaction, along with analogous formation pathways of other natural amino acids, is accompanied by competing reactions yielding alternative products, potentially diminishing serine formation. Alternative interstellar formation pathways for serine are proposed, which could be experimentally tested by future laboratory studies.

Amino Acid Ionic Liquid Coated Magnetic Core Fe<sub>3</sub>O<sub>4</sub>@SiO<sub>2</sub> Nanoparticles Coupled with UV Spectrophotometry for the Separation /Analysis Congo Red

Congo red has strong tinting strength, low price that it was used in meat dyeing. Amino acid ionic liquids (AAILs) containing amino acid cations or anions are synthesized from natural amino acids, which has the characteristics of low toxicity. Nowadays, Fe<sub>3</sub>O<sub>4</sub>@SiO<sub>2</sub>@AAIL composites has seemly not been reported for the separation/analysis of congo red. In this work, Fe<sub>3</sub>O<sub>4</sub>@SiO<sub>2</sub>@AAIL nanoparticles were used as magnetic solid phase adsorbents in combination with UV spectrophotometry for separation of congo red.

Catalytically Active SiO2 Aerogels Comprising Chelate Complexes of Palladium.

A series of silica-based aerogels comprising novel bifunctional chelating ligands was prepared. To produce target aerogels, two aminosilanes, namely (3-aminopropyl)trimethoxysilane (APTMS) and N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (AEAPTMS), were acylated by natural amino acids ((S)-(+)-2-phenylglycine or L-phenylalanine), followed by gelation and supercritical drying (SCD). Lithium tetrachloropalladate was used as the metal ion source to prepare strong complexes of Pd2+ with amino acids covalently bonded to a silica matrix. Aerogels bearing chelate complexes retain the Pd2+ oxidation state after supercritical drying in CO2, but the Pd ion is reduced to Pd metal after SCD in isopropanol. Depending on the structure of amino complexes, Pd-containing aerogels showed catalytic activity and selectivity in the hydrogenation reactions of C=C, C≡C and C=O bonds.

Rapid room-temperature phosphorescence chiral recognition of natural amino acids

Chiral recognition of amino acids is very important in both chemical and life sciences. Although chiral recognition with luminescence has many advantages such as being inexpensive, it is usually slow and lacks generality as the recognition module relies on structural complementarity. Here, we show that one single molecular-solid sensor, L-phenylalanine derived benzamide, can manifest the structural difference between the natural, left-handed amino acid and its right-handed counterpart via the difference of room-temperature phosphorescence (RTP) irrespective of the specific chemical structure. To realize rapid and reliable sensing, the doped samples are obtained as nanocrystals from evaporation of the tetrahydrofuran solutions, which allows for efficient triplet-triplet energy transfer to the chiral analytes generated in situ from chiral amino acids. The results show that L-analytes induce strong RTP, whereas the unnatural D-analytes produce barely any afterglow. The method expands the scope of luminescence chiral sensing by lessening the requirement for specific molecular structures.

Efficient Transferase Engineering for SAM Analog Synthesis from Iodoalkanes.

S-Adenosyl-l-methionine (SAM) is an important cosubstrate in various biochemical processes, including selective methyl transfer reactions. Simple methods for the (re)generation of SAM analogs could expand the chemistry accessible with SAM-dependent transferases and go beyond methylation reactions. Here we present an efficient enzyme engineering strategy to synthesize different SAM analogs from "off-the-shelf" iodoalkanes through enzymatic alkylation of S-adenosyl-l-homocysteine (SAH). This was achieved by mutating multiple hydrophobic and structurally dynamic amino acids simultaneously. Combinatorial mutagenesis was guided by the natural amino acid diversity and generated a highly functional mutant library. This approach increased the speed as well as the scale of enzyme engineering by providing a panel of optimized enzymes with orders of magnitude higher activities for multiple substrates in just one round of enzyme engineering. The optimized enzymes exhibit catalytic efficiencies up to 31 M-1 s-1, convert various iodoalkanes, including substrates bearing cyclopropyl or aromatic moieties, and catalyze S-alkylation of SAH with very high stereoselectivities (>99 % de). We further report a high throughput chromatographic screening system for reliable and rapid SAM analog analysis. We believe that the methods and enzymes described herein will further advance the field of selective biocatalytic alkylation chemistry by enabling SAM analog regeneration with "off-the-shelf" reagents.

Stereochemical Behavior of Pyrrolo-Pyrazole Peptidomimetics Promoting Phase-Selective Supramolecular Organogels.

Supramolecular gels were developed by taking advantage of an assembly of small dipeptides containing pyrrolo-pyrazole scaffolds. The dipeptides were prepared through a robust and ecofriendly synthetic approach from the commercially available starting materials of diazoalkanes and maleimides. By playing with the functionalization of the scaffold, the choice of the natural amino acid, and the stereochemistry, we were able to obtain phase-selective gels. In particular, one peptidomimetic showed gelation ability and thermoreversibility in aromatic solvents at very low concentrations. Rheology tests showed a typical viscoelastic solid profile, indicating the formation of strong gels that were stable under high mechanical deformation. NMR studies were performed, allowing us to determine the conformational and stereochemical features at the base of the supramolecular interactions.

New Transferrin Receptor-Targeted Peptide-Doxorubicin Conjugates: Synthesis and In Vitro Antitumor Activity.

Poor selectivity to tumor cells is a major drawback in the clinical application of the antitumor drug doxorubicin (DOX). Peptide-drug conjugates (PDCs) constructed by modifying antitumor drugs with peptide ligands that have high affinity to certain overexpressed receptors in tumor cells are increasingly assessed for their possibility of tumor-selective drug delivery. However, peptide ligands composed of natural L-configuration amino acids have the defects of easy enzymatic degradation and insufficient biological stability. In this study, two new PDCs (LT7-SS-DOX and DT7-SS-DOX) were designed and synthesized by conjugating a transferrin receptor (TfR) peptide ligand LT7 (HAIYPRH) and its retro-inverso analog DT7 (hrpyiah), respectively, with DOX via a disulfide bond linker. Both conjugates exhibited targeted antiproliferative effects on TfR overexpressed tumor cells and little toxicity to TfR low-expressed normal cells compared with free DOX. Moreover, the DT7-SS-DOX conjugate possessed higher serum stability, more sustained reduction-triggered drug release characteristics, and stronger in vitro antiproliferative activity as compared to LT7-SS-DOX. In conclusion, the coupling of antitumor drugs with the DT7 peptide ligand can be used as a promising strategy for the further development of stable and efficient PDCs with the potential to facilitate TfR-targeted drug delivery.

Composition and Conformation of Hetero- versus Homo-Fluorinated Triazolamers Influence their Activity on Islet Amyloid Polypeptide Aggregation.

Novel fluorinated foldamers based on aminomethyl-1,4-triazolyl-difluoroacetic acid (1,4-Tz-CF2) units were synthesized and their conformational behaviour was studied by NMR and molecular dynamics. Their activity on the aggregation of the human islet amyloid polypeptide (hIAPP) amyloid protein was evaluated by fluorescence spectroscopy and mass spectrometry. The fluorine labelling of these foldamers allowed the analysis of their interaction with the target protein. We demonstrated that the preferred extended conformation of homotriazolamers of 1,4-Tz-CF2 unit increases the aggregation of hIAPP, while the hairpin-like conformation of more flexible heterotriazolamers containing two 1,4-Tz-CF2 units mixed with natural amino acids from the hIAPP sequence reduces it, and more efficiently than the parent natural peptide. The longer heterotriazolamers having three 1,4-Tz-CF2 units adopting more folded hairpin-like and ladder-like structures similar to short multi-stranded β-sheets have no effect. This work demonstrates that a good balance between the structuring and flexibility of these foldamers is necessary to allow efficient interaction with the target protein.

Tryptophanyl-tRNA synthetase-1 (WARS-1) depletion and high tryptophan concentration lead to genomic instability in Caenorhabditis elegans

The fidelity of translation is ensured by a family of proteins named aminoacyl-tRNA synthetases (ARSs), making them crucial for development and survival. More recently, mutations in the tryptophanyl-tRNA synthetase 1 (WARS1) have been linked to various human diseases, from intellectual disability to various types of cancer. To understand the function of WARS1, we investigated the effect of WARS-1 depletion during the mitotic and meiotic cell cycle in the developing germline of Caenorhabditis elegans (C. elegans) and demonstrated the role of WARS-1 in genome integrity. wars-1 knockdown results in cell cycle arrest of the mitotically active germ cells. Such mitotic arrest is also associated with canonical DNA damage-induced checkpoint signaling in mitotic and meiotic germ cells. Significantly, such DNA checkpoint activation is associated with the morphological anomalies in chromatin structures that are the hallmarks of genome instability, such as the formation of chromatin bridges, micronuclei, and chromatin buds. We demonstrated that knocking down wars-1 results in an elevation of the intracellular concentration of tryptophan and its catabolites, a surprising finding emphasizing the impact of cellular amino acid availability and organismal/individual dietary uptake on genome integrity. Our result demonstrates that exposing C. elegans to a high tryptophan dosage leads to DNA damage checkpoint activation and a significant increase in the tryptophan metabolites. Targeting tryptophan catabolism, the least utilized amino acid in nature, can be important in developing new cancer therapeutic approaches. All in all, we have strong evidence that knocking down wars-1 results in defects in genomic integrity.

Methacrylated gelatin hydrogel conjugated with ε-polylysine and enriched with platelet-rich plasma for chronically infected wounds

While numerous hydrogel dressings are available for treating chronically infected wounds, their clinical application is impeded by intricate preparation processes, low mechanical strength, and frequent reliance on exogenous antimicrobial agents. The latter often leads to antibiotic misuse and compromises the bioactivity of cell growth-promoting substances. Therefore, the field of therapeutic treatment is faced with a pressing need to prepare high-mechanical-strength hydrogels through a facile procedure, achieving endogenous antibacterial characteristics and long-term healing abilities for chronically infected wounds. In this study, employing the Michael addition reaction principle, we conducted the conjugate addition of the natural antimicrobial poly amino acid, ε-polylysine (ε-PL), to gelatin methacrylate. This not only augmented the hydrogel’s mechanical strength but also preserved its antimicrobial efficacy. Subsequently, platelet-rich plasma (PRP), capable of releasing diverse growth factors, was introduced. Injectable and degradable hydrogels with high mechanical strength and water absorption were prepared through UV curing while retaining PRP bioactivity. The combination of PRP and ε-PL substantiated the enhanced antimicrobial properties and promotion of human umbilical vein endothelial cell growth, as validated through bacterial inhibition experiments, such as live-dead bacterial staining and cellular assays, including cell proliferation. Therefore, the as-developed PL-PRP hydrogel presents as a promising hydrogel dressing for the treatment of chronically infected wounds.

Cysteine-based antifouling superhydrophilic membranes prepared via facile thiol-ene click chemistry for efficient oil-water separation

Superhydrophilic membranes with underwater superoleophobicity for oil-water separation have been attracted widely attention. Nevertheless, oil contamination of such membranes represents a pressing challenge in this field. Superhydrophilic/underwater superoleophobic membranes with surface zwitterionic moieties are proved to show excellent antifouling properties; however, such zwitterionic surface modifiers adopted previously usually face the problem of cumbersome synthesis relying on expensive reagents and complicated procedures, accompanied with poor acid/alkali resistance due to the unstable linkers, restricting their practical applications. Herein, we describe an alternative strategy for fabricating antifouling superhydrophilic/underwater superoleophobic membranes from a natural amino acid. Sand particle-based sintered glass membranes were firstly coated with silicone nanofilaments using vinyltrichlorosilane as a precursor through chemical vapor deposition; and then the surfaces of silicone nanofilaments were further functionalized with cysteine via thiol-ene click chemistry. The resulting membranes exhibited high separation flux and efficiency for gravity-driven separation of various oil-water mixtures and surfactant-stabilized oil-in-water emulsions. Moreover, such membranes displayed excellent antifouling properties and were reusable for the separation of oil-water mixtures and surfactant-stabilized oil-in-water emulsions. With the advantages of facile fabrication, low-cost, fouling resistance and high separation performance, we believe that cysteine-based glass membranes without any hydrolytic bonds will arouse tremendous attentions for oil-water separation.

Visible Light‐Mediated Defluorination to Access 1,1‐Difluoro‐1,3‐Enynes

Herein, a visible light‐mediated defluorination reaction to access 1,1‐difluoro‐1,3‐enynes is described. Compared with previous studies, this protocol employs more readily accessible acids as a radical precursor under the redox‐neutral conditions. Moreover, the reaction exhibits high compatibility with diverse primary, secondary and tertiary acids, especially natural amino acids and drug‐derived acids. Preliminary mechanism investigations reveal that a radical pathway is involved in the catalytic cycle.

Click preparation of triazole-bridged teicoplanin-bound chiral stationary phases for efficient separating amino acid enantiomers

Enantioseparation of amino acids is considered as a challenging task due to the extreme structural similarity of their enantiomers. Herein, teicoplanin was modified with different chemical equivalents of azide groups and attached to silica particles by employing Click Chemistry for resolution of chiral amino acids for the first time. Interestingly, teicoplanin modified with 5-fold the chemical equivalent of azide groups (TK-2 CSP) exhibited superior amino acid separation ability compared to two other columns: one modified with only 1-fold the chemical equivalent of azide groups (TK-1 CSP), and the other modified with excess azide groups (TK-3 CSP). Additionally, the TK-2 CSP exhibited superior enantioselectivity when separating amino acids containing hydrophobic alkyl side chains in comparison to other teicoplanin-based CSPs. The TK-2 CSP column allows the baseline separation of 7 native amino acids. Molecular docking demonstrates that effective enantioseparation arises from distinct patterns of interaction between the host and guest molecules. Moreover, (p-methyl) phenylcarbaminoylated-teicoplanin CSP (TK-4, TK-5 CSP) were prepared by post-modification from TK-1 CSP and TK-2 CSP to isolate Fmoc-modified amino acids. This work explores the impact of various modification methods on the enantioseparation effects of host molecules and paves the way for expanding the potential applications of teicoplanin and macrocyclic glycopeptide molecules.