scholarly journals New Morphiceptin Peptidomimetic Incorporating (1S,2R,3S,4S,5R)-2-Amino-3,4,5-trihydroxycyclopen-tane-1-carboxylic acid: Synthesis and Structural Study

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2574
Author(s):  
Raquel Soengas ◽  
Marcos Lorca ◽  
Begoña Pampín ◽  
Víctor M. Sánchez-Pedregal ◽  
Ramón J. Estévez ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Carboxylic Acid ◽  
Structural Study ◽  
Acid Synthesis ◽  
Analgesic Drug ◽  
Proline Residue ◽  
Docking Calculations ◽  
A Subunit

We present the synthesis and structural study of a new peptidomimetic of morphiceptin, which can formally be considered as the result of the replacement of the central proline residue of this natural analgesic drug with a subunit of (1S,2R,3S,4S,5R)-2-amino-3,4,5-trihydroxycyclopentane-1-carboxylic acid, previously obtained from L-idose. An optimized synthesis of this trihydroxylated cispentacin derivative is also reported. Molecular docking calculations on the target receptor support a favorable role of the hydroxy substituents of the non-natural β-amino acid incorporated into the peptidomimetic.

Isolated complexes of the amino acid arginine with polyether and polyamine macrocycles, the role of proton transfer

2017 ◽  
Vol 19 (46) ◽  
pp. 31345-31351 ◽  
Author(s):  
Juan Ramón Avilés-Moreno ◽  
Giel Berden ◽  
Jos Oomens ◽  
Bruno Martínez-Haya
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Proton Transfer ◽  
Acid Group ◽  
Side Group ◽  
Carboxylic Acid Group

Protonated arginine interacts with 12-crown-4 through the guanidinium side group. In the complex with the N-substituted analog cyclen, the dominant conformation is the result of the proton transfer from the carboxylic acid group of the amino acid to the macrocycle.

scholarly journals Role of the DksA-Like Protein in the Pathogenesis and Diverse Metabolic Activity of Campylobacter jejuni

2008 ◽  
Vol 190 (13) ◽  
pp. 4512-4520 ◽  
Author(s):  
Jiae Yun ◽  
Byeonghwa Jeon ◽  
Yi-Wen Barton ◽  
Paul Plummer ◽  
Qijing Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Campylobacter Jejuni ◽  
Pathogenic Bacteria ◽  
Acid Metabolism ◽  
Acid Synthesis ◽  
Regulatory Role ◽  
Intestinal Cells ◽  
Amino Acid Synthesis ◽  
Metabolic Reactions

ABSTRACT DksA is well known for its regulatory role in the transcription of rRNA and genes involved in amino acid synthesis in many bacteria. DksA has also been reported to control expression of virulence genes in pathogenic bacteria. Here, we elucidated the roles of a DksA-like protein (CJJ81176_0160, Cj0125c) in the pathogenesis of Campylobacter jejuni. As in other bacteria, transcription of stable RNA was repressed by the DksA-like protein under stress conditions in C. jejuni. Transcriptomic and proteomic analyses of C. jejuni 81-176 and an isogenic mutant lacking the DksA-like protein showed differential expression of many genes involved in amino acid metabolism, iron-related metabolism, and other metabolic reactions. Also, the C. jejuni DksA-like protein mutant exhibited a decreased ability to invade intestinal cells and induce release of interleukin-8 from intestinal cells. These results suggest that the DksA-like protein plays an important regulatory role in diverse metabolic events and the virulence of C. jejuni.

Role of O-acetylhomoserine sulfhydrylase in sulfur amino acid synthesis in various yeasts

Yeast ◽  
1993 ◽  
Vol 9 (12) ◽  
pp. 1335-1342 ◽  
Author(s):  
Jerzy Brzywczy ◽  
Andrzej Paszewski
Keyword(s):  
Amino Acid ◽  
Acid Synthesis ◽  
Sulfur Amino Acid ◽  
Amino Acid Synthesis

An Expansion of the Role of the Corey - Link Reaction for the Synthesis of α-Substituted Carboxylic Acid Esters

2006 ◽  
Vol 59 (7) ◽  
pp. 426 ◽  
Author(s):  
Adrian Scaffidi ◽  
Brian W. Skelton ◽  
Robert V. Stick ◽  
Allan H. White
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Methyl Ester ◽  
Single Crystal ◽  
X Ray ◽  
Structure Determinations ◽  
Acid Esters

The treatment of 1,2:5,6-di-O-isopropylidene-α-d-ribo-hexos-3-ulose with chloroform under basic conditions has yielded the normal 3-C-trichloromethyl-α-d-allofuranose derivative. Under the conditions of the modified Corey–Link reaction but with a nucleophile different from the usual azide, a range of α-substituted carboxylic acid esters (and one amide) has been obtained. A similar addition of bromoform to the ulose has formed the α-bromo methyl ester. Two attempts at forming an ‘inositol α-amino acid’ from a polyhydroxylated cyclohexanone failed. Single-crystal X-ray structure determinations are reported for (3S)-1,2:5,6-di-O-isopropylidene-3-C-methoxycarbonyl-3-S-phenyl-3-thio-α-d-ribo-hexose, (3S)-1,2:5,6-di-O-isopropylidene-3-S-phenyl-3-C-(phenylthio)carbonyl-3-thio-α-d-ribo-hexose, 3-deoxy-1,2:5,6-di-O-isopropylidene-3-C-methoxycarbonyl-α-d-erythro-hex-3-enofuranose, 4,6-di-O-benzyl-2-C-trichloromethyl-scyllo-inositol 1,3,5-orthoformate, 2,2'-anhydro-4,6-di-O-benzyl-2-C-dichlorohydroxymethyl-scyllo-inositol 1,3,5-orthoformate, 1,3,4,5,6-penta-O-benzyl-2-C-trichloromethyl-myo-inositol, and 2-amino-1,3,4,5,6-penta-O-benzyl-2-C-cyano-2-deoxy-myo-inositol.

Exploring the Role of Water Molecules in the Ligand Binding Domain of PDE4B and PDE4D: Virtual Screening Based Molecular Docking of Some Active Scaffolds

2019 ◽  
Vol 15 (4) ◽  
pp. 334-366
Author(s):  
Priya Singh ◽  
Mitali Mishra ◽  
Shivangi Agarwal ◽  
Samaresh Sau ◽  
Arun K. Iyer ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Water Molecule ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Water Molecules ◽  
Docking Experiment

Background: The phosphodiesterase (PDE) is a superfamily represented by four genes: PDE4A, B,C, and D which cause the hydrolysis of phosphodiester bond of cAMP to yield inactive AMP. c-AMP catalyzing enzyme is predominant in inflammatory and immunomodulatory cells. Therapy to treat Chronic Obstructive Pulmonary Disease (COPD) with the use of PDE4 inhibitors is highly envisaged. Objective: A molecular docking experiment with large dataset of diverse scaffolds has been performed on PDE4 inhibitors to analyze the role of amino acid responsible for binding and activation of the secondary transmitters. Apart from the general docking experiment, the main focus was to discover the role of water molecules present in the ligand-binding domain. Methods: All the compounds were docked in the PDE4B and PDE4D active cavity to produce the free binding energy scores and spatial disposition/orientation of chemical groups of inhibitors around the cavity. Under uniform condition, the experiments were carried out with and without water molecules in the LBD. The exhaustive study was carried out on the Autodock 4.2 software and explored the role of water molecules present in the binding domain. Results: In presence of water molecule, Roflumilast has more binding affinity (-8.48 Kcal/mol with PDE4B enzyme and -8.91 Kcal/mol with PDE4D enzyme) and forms two hydrogen bonds with Gln443 and Glu369 and amino acid with PDE4B and PDE4D enzymes respectively. While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed. Similar observation was made with clinically tested molecules. Conclusion: In protein-ligand binding interactions, appropriate selection of water molecules facilitated the ligand binding, which eventually enhances the efficiency as well as the efficacy of ligand binding.

scholarly journals Ion Channels Involved in Substance P-Mediated Nociception and Antinociception

2019 ◽  
Vol 20 (7) ◽  
pp. 1596 ◽  
Author(s):  
Chu-Ting Chang ◽  
Bo-Yang Jiang ◽  
Chih-Cheng Chen
Keyword(s):  
Amino Acid ◽  
Ion Channels ◽  
Substance P ◽  
Drug Development ◽  
Cell Types ◽  
Analgesic Drug ◽  
Differential Cell ◽  
Neurokinin 1

Substance P (SP), an 11-amino-acid neuropeptide, has long been considered an effector of pain. However, accumulating studies have proposed a paradoxical role of SP in anti-nociception. Here, we review studies of SP-mediated nociception and anti-nociception in terms of peptide features, SP-modulated ion channels, and differential effector systems underlying neurokinin 1 receptors (NK1Rs) in differential cell types to elucidate the effect of SP and further our understanding of SP in anti-nociception. Most importantly, understanding the anti-nociceptive SP-NK1R pathway would provide new insights for analgesic drug development.

scholarly journals The Role of the Tricarboxylic Acid Cycle in Amino Acid Synthesis in Escherichia Coli

1953 ◽  
Vol 39 (10) ◽  
pp. 1013-1019 ◽  
Author(s):  
R. B. Roberts ◽  
D. B. Cowie ◽  
R. Britten ◽  
E. Bolton ◽  
P. H. Abelson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Tricarboxylic Acid Cycle ◽  
Acid Synthesis ◽  
Tricarboxylic Acid ◽  
Amino Acid Synthesis ◽  
Acid Cycle

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

Microbiology ◽  
2004 ◽  
Vol 150 (9) ◽  
pp. 2911-2920 ◽  
Author(s):  
Keitarou Kimura ◽  
Lam-Son Phan Tran ◽  
Yoshifumi Itoh
Keyword(s):  
Bacillus Subtilis ◽  
Amino Acid ◽  
Minimal Medium ◽  
Degradation Products ◽  
Acid Synthesis ◽  
Rich Medium ◽  
Amino Acid Synthesis ◽  
Double Mutation ◽  
Glutamate Racemase

Many bacteria, including Escherichia coli, have a unique gene that encodes glutamate racemase. This enzyme catalyses the formation of d-glutamate, which is necessary for cell wall peptidoglycan synthesis. However, Bacillus subtilis has two glutamate racemase genes, named racE and yrpC. Since racE appears to be indispensable for growth in rich medium, the role of yrpC in d-amino acid synthesis is vague. Experiments with racE- and yrpC-knockout mutants confirmed that racE is essential for growth in rich medium but showed that this gene was dispensable for growth in minimal medium, where yrpC executes the anaplerotic role of racE. LacZ fusion assays demonstrated that racE was expressed in both types of media but yrpC was expressed only in minimal medium, which accounted for the absence of yrpC function in rich medium. Neither racE nor yrpC was required for B. subtilis cells to synthesize poly-γ-dl-glutamate (γ-PGA), a capsule polypeptide of d- and l-glutamate linked through a γ-carboxylamide bond. Wild-type cells degraded the capsule during the late stationary phase without accumulating the degradation products, d-glutamate and l-glutamate, in the medium. In contrast, racE or yrpC mutant cells accumulated significant amounts of d- but not l-glutamate. Exogenous d-glutamate utilization was somewhat defective in the mutants and the double mutation of race and yrpc severely impaired d-amino acid utilization. Thus, both racemase genes appear necessary to complete the catabolism of exogenous d-glutamate generated from γ-PGA.

scholarly journals Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Wankui Jiang ◽  
Chenfei Zhang ◽  
Qinqin Gao ◽  
Mingliang Zhang ◽  
Jiguo Qiu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Degradation Mechanism ◽  
Catalytic Efficiency ◽  
Acid Sites ◽  
Amino Acid Residues ◽  
Content Type ◽  
Key Enzyme ◽  
A Subunit ◽  
Hydrolysis Of

ABSTRACT Methomyl {bis[1-methylthioacetaldehyde-O-(N-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed ameH. A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from Schizosaccharomyces pombe ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. Km and kcat of AmeH for methomyl were 87.5 μM and 345.2 s−1, respectively, and catalytic efficiency (kcat/Km) was 3.9 μM−1 s−1. Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations. IMPORTANCE Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as cehA, mcbA, cahA, and mcd, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, ameH, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.

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