Glutamic Acid Analogues Research Articles

Potential neurotoxicity of αlfa-amino adipic acid, a marker of protein oxidation in ultra-processed foods, and analogue of neurotransmitter glutamic acid

Potential neurotoxicity of αlfa-amino adipic acid, a marker of protein oxidation in ultra-processed foods, and analogue of neurotransmitter glutamic acid

Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid

AbstractGenetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.

Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid.

Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.

Semisynthesis of Glutamine-Methylated Proteins Enabled by Genetic Code Expansion.

Gln methylation is a newly identified histone mark and mediates ribosomal biogenesis. Site-specifically Gln-methylated proteins are valuable tools to elucidate the biological implications of this modification. Herein, we describe a protocol to generate histones with site-specific Gln methylation in a semisynthetic manner. Firstly, an esterified glutamic acid analogue (BnE) is genetically encoded into proteins by genetic code expansion with high efficiency, which can be quantitatively converted into an acyl hydrazide via hydrazinolysis. Then, through a reaction with acetyl acetone, the acyl hydrazide is converted to reactive Knorr pyrazole. Finally, the in situ generated Knorr pyrazole is incubated with methylamine to give Gln methylation.

A stereochemical journey around spirocyclic glutamic acid analogs.

A practical divergent synthetic approach is reported for the library of regio- and stereoisomers of glutamic acid analogs built on the spiro[3.3]heptane scaffold. Formation of the spirocyclic scaffold was achieved starting from a common precursor - an O-silylated 2-(hydroxymethyl)cyclobutanone derivative. Its olefination required using the titanium-based Tebbe protocol since the standard Wittig reaction did not work with this particular substrate. The construction of the second cyclobutane ring of the spirocyclic system was achieved through either subsequent dichloroketene addition or Meinwald oxirane rearrangement as the key synthetic steps, depending on the substitution patterns in the target compounds (1,6- or 1,5-, respectively). Further modified Strecker reaction of the resulting racemic spirocyclic ketones with the Ellman's sulfinamide as a chiral auxiliary had low to moderate diastereoselectivity; nevertheless, all stereoisomers were isolated in pure form via chromatographic separation, and their absolute configuration was confirmed by X-ray crystallography. Members of the library were tested for the inhibitory activity against H. pylori glutamate racemase.

Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain - binding peptide macrocycles.

Targeting protein – protein interactions (PPIs) has emerged as an important area of discovery for anticancer therapeutic development. In the case of phospho-dependent PPIs, such as the polo-like kinase 1 (Plk1) polo-box domain (PBD), a phosphorylated protein residue can provide high-affinity recognition and binding to target protein hot spots. Developing antagonists of the Plk1 PBD can be particularly challenging if one relies solely on interactions within and proximal to the phospho-binding pocket. Fortunately, the affinity of phospho-dependent PPI antagonists can be significantly enhanced by taking advantage of interactions in both the phospho-binding site and hidden “cryptic” pockets that may be revealed on ligand binding. In our current paper, we describe the design and synthesis of macrocyclic peptide mimetics directed against the Plk1 PBD, which are characterized by a new glutamic acid analog that simultaneously serves as a ring-closing junction that provides accesses to a cryptic binding pocket, while at the same time achieving proper orientation of a phosphothreonine (pT) residue for optimal interaction in the signature phospho-binding pocket. Macrocycles prepared with this new amino acid analog introduce additional hydrogen-bonding interactions not found in the open-chain linear parent peptide. It is noteworthy that this new glutamic acid-based amino acid analog represents the first example of extremely high affinity ligands where access to the cryptic pocket from the pT-2 position is made possible with a residue that is not based on histidine. The concepts employed in the design and synthesis of these new macrocyclic peptide mimetics should be useful for further studies directed against the Plk1 PBD and potentially for ligands directed against other PPI targets.

Diverse protein manipulations with genetically encoded glutamic acid benzyl ester.

Site-specific modification of proteins has significantly advanced the use of proteins in biological research and therapeutics development. Among various strategies aimed at this end, genetic code expansion (GCE) allows structurally and functionally distinct non-canonical amino acids (ncAAs) to be incorporated into specific sites of a protein. Herein, we genetically encode an esterified glutamic acid analogue (BnE) into proteins, and demonstrate that BnE can be applied in different types of site-specific protein modifications, including N-terminal pyroglutamation, caging Glu in the active site of a toxic protein, and endowing proteins with metal chelator hydroxamic acid and versatile reactive handle acyl hydrazide. Importantly, novel epigenetic mark Gln methylation is generated on histones via the derived acyl hydrazide handle. This work provides useful and unique tools to modify proteins at specific Glu or Gln residues, and complements the toolbox of GCE.

The Arsenic Methylation Cycle: How Microbial Communities Adapted Methylarsenicals for Use as Weapons in the Continuing War for Dominance

Arsenic is the most ubiquitous environmental toxin. Most microorganisms have evolved mechanisms to use methylarsenicals as weapons in microbial warfare. This has created cycles of arsenic methylation and demethylation, which constitutes an important part of arsenic biogeochemical cycles and environmental health. Arsenic methylation forms methylarsenite (MAs(III)), arsenobetaine, arsenosugars and the new identified methylarsenical antibiotic, arsinothricin (AST). Bacteria use MAs(III) and AST to gain a competitive advantage over other bacteria. Microbes generate toxic MAs(III) by 1) methylation of arsenite (As(III)) or 2) reduction of methylarsenate (MAs(V)). In air MAs(III) is oxidized to MAs(V), making methylation an detoxification process in aerobes. MAs(V) is continually re-reduced to MAs(III) by other bacteria, giving them a competitive advantage over sensitive bacteria. Because generation of a sustained pool of MAs(III) requires microbial communities, these complex interactions are an emergent property, that is, overall scheme of arsenic-containing antibiotics emerges from interaction of multiple species. In response to production of the antibiotic MAs(III), other members of microbial communities have evolved at least four mechanisms for resistance to MAs(III): 1) ArsH detoxifies MAs(III) by oxidation to nontoxic MAs(V); 2) ArsI degrades MAs(III) by cleavage of the C-As bond to form less toxic As(III); 3) the ArsP efflux permease confers selective resistance to MAs(III); and 4) the unrelated ArsK efflux permease confers resistance to both trivalent inorganic and organoarsenicals. Environmental application of anthropogenic aromatic arsenicals further fuels bacterial warfare and selection for novel resistance mechanisms. In another microbial adaptation to use environmental arsenic as a weapon, some soil bacteria synthesize a methylarsenate analog of the amino acid glutamic acid termed arsinothricin (AST); AST shows a broad-spectrum antibiotic action against both Gram-negative and Gram-positive bacteria. In response to the environmental challenge presented by AST, arsN genes evolved to detoxify it by acetylation of the α-amino group. Thus life has adapted to use environmental arsenic as a weapon in the continuing battle for dominance. Both MAs(III) and AST are natural products with antibiotic-like properties, both are toxic methylarsenicals produced by one microbe to kill off competitors, and resistances have arisen for both.

Conformational changes in glutaminyl-tRNA synthetases upon binding of the substrates and analogs using molecular docking and molecular dynamics approaches

Aminoacyl-tRNA synthetases (aaRSs) are considered as important components in protein translation as they facilitate the attachment of specific transfer RNA (tRNA) to form aminoacyl-tRNAs. Our study focused on understanding the crystal structure of Glutaminyl-tRNA synthetase (GlnRS) from Thermus thermophilus HB8 (PDB ID:5ZDO) and mechanism of formation of enzyme–substrate complex using substrates and its analogs by applying molecular dynamics simulation (MDS) to investigate the conformational changes. Least energy structure of TtGlnRS was considered to dock the enzyme substrates such as glutamine (Gln), glutamic acid (Glu), adenosine monophosphate (AMP), adenosine triphosphate (ATP), QSI and various substrate analogs (2MA, 4SU and 5MU) onto the active site of the enzyme. We focused on comparative analysis of binding specificity between Gln and Glu; similarly, ATP and AMP. Active site organization as observed by MDS analysis showed interactive changes associated with substrate and catalytically important loops. Study found that when tRNAGln specific for GlnRS was docked into the active site of the TtGlnRS enzyme it interacts with 2' OH on the ribose acceptor end of the tRNA. Upon validation with 50 ns MDS, the maximum deviations and conformational changes of secondary structural elements were observed to be high in the loop regions of enzyme–substrate complexes. Binding affinity of ATP to TtGlnRS was further proved by isothermal titration calorimetry.AbbreviationsaaRSsaminoacyl-tRNA synthetasesAMPadenosine monophosphateATPadenosine triphosphateGlideGrid-based LIgand Docking with EnergeticGlnRSglutaminyl-tRNA synthetaseGRAVYGRand AVerage of hydropathicitYGROMACSGROingen Machine for Chemical SimulationsHADDOCKHigh Ambiguity Driven protein–protein DOCKingITCisothermal titration calorimetry2MA2-methyladenosine 5'-(dihydrogen phosphate)MDSmolecular dynamics simulation5MU5-methyluridine 5'-monophosphateNPTnumber of particles, pressure and temperatureNVTnumber of particles, volume and temperatureOPLS-AAoptimized potential for liquid simulation all atomPDBBrookhaven Protein DatabankPMEParticle-Mesh EwaldQSI5'-o-[n-(l-Glutaminyl)-sulfamoyl]adenosineRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuation4SU4-thiouracil 5'-monophosphateSPCsimple point chargetRNAtransfer ribo nucleic acidTtThermus thermophilusXPextra precisionCommunicated by Ramaswamy H. Sarma

Novel synthetic approach to non-natural conformationally rigid spiro-linked amino acids

1-Aminospiro[2.3]hexane-1,5-dicarboxylic and 1-ammo-5-(ammomethyl)spiro[2.3]hexane-1-carboxylic acids, which are the conformationally rigid analogues of glutamic acid and lysine, respectively, were synthesized from 3-methylidenecyclobutanecarbonitrile. The synthetic route includes a catalytic [1+2]-cycloaddition of ethyl 2-diazo-2-nitroacetate to a double bond of the unsaturated nitrile, a subsequent chemoselective reduction of the nitro and cyano groups, and a hydrolysis of the ester moiety.

Synthesis of nonracemic hydroxyglutamic acids.

Glutamic acid is involved in several cellular processes though its role as the neurotransmitter is best recognized. For detailed studies of interactions with receptors a number of structural analogues of glutamic acid are required to map their active sides. This review article summarizes syntheses of nonracemic hydroxyglutamic acid analogues equipped with functional groups capable for the formation of additional hydrogen bonds, both as donors and acceptors. The majority of synthetic strategies starts from natural products and relies on application of chirons having the required configuration at the carbon atom bonded to nitrogen (e.g., serine, glutamic and pyroglutamic acids, proline and 4-hydroxyproline). Since various hydroxyglutamic acids were identified as components of complex natural products, syntheses of orthogonally protected derivatives of hydroxyglutamic acids are also covered.

Protonation States of Glufosinate in Aqueous Solution

Glufosinate, an analogue of glutamic acid (also known as phosphinothricin), is an important herbicide. The protonation constants of glufosinate were determined by means of potentiometric titrations at variable temperatures with ionic strength 0.5 mol·L−1 (NaCl solution). The heat effects of the protonation reactions of glufosinate were measured by direct calorimetry. NMR spectroscopies have demonstrated that the first protonation site occurs on the nitrogen atom in the amino group, followed by one of the oxygen atoms in the phosphono group, and finally the carboxyl oxygen atom. This trend is in good agreement with the enthalpy of protonation and crystal structure results. These data will help to predict the speciation of glufosinate in physiological systems.

Straightforward synthesis of fluorinated amino acids by Michael addition of ethyl bromodifluoroacetate to α,β-unsaturated α-amino acid derivatives

Copper-mediated Michael addition of ethyl bromodifluoroacetate to N-protected α,β-unsaturated α-amino acid esters was applied for straightforward synthesis of γ,γ-difluorinated analogues of glutamic acid (compound 1) and glutamine (compound 10). Moreover, a proline-based, sterically constrained analog of γ,γ-difluoroglutamic acid (compound 24) was prepared.

Multiple molecular modelling studies on some derivatives and analogues of glutamic acid as matrix metalloproteinase-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a potential target in anticancer drug discovery due to its association with angiogenesis, metastasis and tumour progression. In this study, 67 glutamic acid derivatives, synthesized and evaluated as MMP-2 inhibitors, were taken into account for multi-QSAR modelling study (regression-based 2D-QSAR, classification-based LDA-QSAR, Bayesian classification QSAR, HQSAR, 3D-QSAR CoMFA and CoMSIA as well as Open3DQSAR). All these QSAR studies were statistically validated individually. Regarding the 3D-QSAR analysis, the Open3DQSAR results were better than CoMFA and CoMSIA, although all these 3D-QSAR models supported each other. The importance of biphenylsulphonyl moiety over phenylacetyl/naphthylacetyl moieties was established due to its association with favourable steric and hydrophobic characters. HQSAR, LDA-QSAR and Bayesian classification QSAR studies also suggested that the biphenylsulphonamido group was better than the phenylacetylcarboxamido function. Additionally, glutamines were proven to be far better inhibitors than isoglutamines. Observations obtained from the current study were revalidated and supported by the earlier reported molecular modelling studies. Depending on these observations, newer glutamic acid-based compounds may be designed further in future for potent MMP-2 inhibitory activity.

A Glutamic Acid Analog Bearing an Ethylenediamine Moiety Promotes the Cytosolic Delivery of TAT Peptides

The stepwise protonation of ethylenediamine-containing peptides at low pH in endosomes is hypothesized to disrupt the endosomal membrane and enhance cytosolic delivery. Incorporation of a novel glutamic acid analog bearing an ethylenediamine moiety into TAT peptides markedly enhanced cytosolic delivery without cytotoxicity.

Cyclopropyl-containing sulfonyl amino acids: Exploring the enantioseparation through chiral ligand-exchange chromatography

In the scope of a broader study focused on glutamate receptors regulators, we have been engaged in synthesis, analysis and pharmacological characterization of rigid analogues of glutamic acid. These compounds exhibited the bioisosteric replacement of the distal carboxylic group with the sulfonic one. Besides the sophisticated synthetic approach, we targeted preparation of a series of cyclopropyl-containing sulfonyl amino acids and development of a chromatographic enantioselective method suitable for distinguishing and quantifying the resulting isomers. Due to chelating ability, the chiral ligand-exchange chromatography (CLEC) was used for diastereo- and enantioseparation of the synthesized compounds. The CLEC-based enantioseparation was achieved by using a chiral mobile phase (CMP) system with N,N-dimethyl-(S)-phenylalanine [(S)-DMP] as the chiral selector. Only one of the investigated enantiomeric pairs was undiscriminated with the employed CLEC–CMP system which, very importantly, produced the simultaneous diastereo- and enantioseparation of two compounds of the series. Furthermore, the large α and RS values computed for three enantiomer pairs could be a good basis for a successful scale-up to a semi-preparative level.

Convenient syntheses of phosphinic analogues of γ-aminobutyric- and glutamic acids

Three-steps, one-pot synthesis of 2-amino-4-(hydroxyphosphinyl)butyric acid from dibutyl ester of vinylphosphinic acid was carried out with an overall yield of 66%. 3-Aminopropylphosphinic acid was prepared from allylamine in three steps with an overall yield of 56%. These improved protocols allowed to obtain these commercially unavailable phosphinic analogues of glutamic acid and GABA for testing on potential molecular targets.

Novel bicyclo[3.1.0]hexane analogs as antagonists of metabotropic glutamate 2/3 receptors for the treatment of depression

Negative modulators of metabotropic glutamate 2 & 3 receptors demonstrate antidepressant-like activity in animal models and hold promise as novel therapeutic agents for the treatment of major depressive disorder. Herein we describe our efforts to prepare and optimize a series of conformationally constrained 3,4-disubstituted bicyclo[3.1.0]hexane glutamic acid analogs as orthosteric (glutamate site) mGlu2/3 receptor antagonists. This work led to the discovery of a highly potent and efficacious tool compound 18 (hmGlu2 IC50 46±14.2nM, hmGlu3 IC50=46.1±36.2nM). Compound 18 showed activity in the mouse forced swim test with a minimal effective dose (MED) of 1mg/kg ip. While in rat EEG studies it exhibited wake promoting effects at 3 and 10mg/kg ip without any significant effects on locomotor activity. Compound 18 thus represents a novel tool molecule for studying the impact of blocking mGlu2/3 receptors both in vitro and in vivo.

An investigation of the role of the adiponectin variable domain on the stability of the collagen‐like domain

The chemical synthesis is described of a polypeptide construct possessing both the variable and the collagen-like domain of adiponectin, which can be used as a model system for probing the influence of the variable domain on multimerization of this important circulating hormone. Using a collagen domain repeat peptide unit derived from native adiponectin or a glutamic acid analogue was ineffective due to noncollagenous conformational properties in both cases. However, employing a collagen model peptide and linking this to the variable domain thioester peptide using native chemical ligation proved effective. The 63 residue peptide was characterized by circular dichroism and mass spectrometry which demonstrated that a collagen-like triple-helical structure was preserved.

ChemInform Abstract: Synthesis of Amino Acids of Cyclopropylglycine Series

AbstractReview: 129 refs.