Newsletter 02/2021

We are happy to announce that the 

will be activated in the online mode. The School is organized by our member Loredano Pollegioni. See https://bsne.lakecomoschool.org/

Do you have news concerning the D-amino acids field to announce? Is there a relevant published paper to mention? Write us and take the advantage of this bimonthly Newsletter.

The Editor’s pick selection of the most intriguing papers is highlighted in yellow.

D-AAs AND PHYSIOLOGY:

• Plasma D-glutamate levels for detecting mild cognitive impairment and Alzheimer’s disease: Machine learning approaches

Chang CH, Lin CH, Liu CY, Huang CS, Chen SJ, Lin WC, Yang HT, Lane HY. 
J Psychopharmacol. 2021 Mar;35(3):265-272. doi: 10.1177/0269881120972331. 

In this study the levels of D-glutamate were determined in peripheral plasma of healthy individuals (31) and patients with mild cognitive impairment (MCI, 21) and Alzheimer’s disease (AD, 133) by HPLC analysis.  The MCI and AD groups showed lower D-glutamate levels compared to healthy controls. Multivariate regression analysis indicated that D-glutamate levels were significantly associated with the total Mini-Mental Status Examination score. The peripheral plasma D-glutamate levels may represent a suitable peripheral biomarker for detecting MCI and AD: machine learning algorithms may assist physicians in this diagnosis. MORE

• Converging evidence on D-amino acid oxidase-dependent enhancement of hippocampal firing activity and passive avoidance learning in rats. 

Nagy LV, Bali ZK, Kapus G, Pelsőczi P, Farkas B, Lendvai B, Lévay G, Hernádi 
I. Int J Neuropsychopharmacol. 2020 Dec 11:pyaa095. doi: 10.1093/ijnp/pyaa095.

This paper focuses on a novel DAAO inhibitor (Compound 30, CPD30) and its positive neurocognitive effects in rat as animal model. DAAO inhibitors are of main interest since they were shown to induce an increase in brain D-serine levels and, as a consequence, to improve neuronal communication and alleviate the symptoms of neuropsychiatric disorders. The authors’ findings uncover a relationship between the neural and behavioral action of DAAO inhibition: by pharmacological treatments, in vivo electrophysiology and behavioural studies they demonstrate that CPD30 increases activity and responsiveness of hippocampal neurons, thus improving memory in an aversive conditioning task. MORE

• Acute D-Serine Co-Agonism of β-Cell NMDA Receptors Potentiates Glucose-Stimulated Insulin Secretion and Excitatory β-Cell Membrane Activity. 

Lockridge A, Gustafson E, Wong A, Miller RF, Alejandro EU. 
Cells. 2021 Jan 7;10(1):E93. doi: 10.3390/cells10010093.

In the past, D-serine (D-Ser) was reported to be produced by serine racemase in human and mouse pancreatic islets, but its acute effect on β-cells NMDA receptors was not investigated. To this aim, Lockridge and co-workers evaluated glucose homeostasis and insulin secretion in mice with a systemic elevation in D-Ser levels. They show that acute and low dose of D-Ser, through NMDA receptors activation, stimulates β-cells excitability and potentiates insulin release, thus exerting an antidiabetic effect. However, the parameters of this regulation appear largely dependent on context (background strain, sex, age, and experimental condition) suggesting a careful choice of experimental conditions to insure mechanistic specificity in the interpretation of outcome. MORE

D-AAs AND BIOFILM:

• D-Serine inhibits the attachment and biofilm formation of methicillin-resistant Staphylococcus aureus.

Iwata Y, Sakai N, Yoneda I, Senda Y, Sakai-Takemori Y, Oshima M, Nakagawa-Yoneda S, Ogura H, Sato K, Minami T, Kitajima S, Toyama T, Yamamura Y, Miyagawa T, Hara A, Shimizu M, Furuichi K, Matsushima K, Wada T.
Biochem Biophys Res Commun. 2021 Jan 22;537:50-56. doi: 10.1016/j.bbrc.2020.12.078.

This paper reports about using D-serine (D-Ser) as a strategy for controlling methicillin-resistant Staphylococcus aureus (MRSA) infection, which represent a serious issue in hospitals. D-Ser resulted effective in reducing bacterial attachment and biofilm formation, two events significantly contributing to the infection initiation. Worthy of note, an inhibitory mechanism was also provided: D-Ser induces the downregulation of genes that play a crucial role in infection. Furthermore, despite D-Ser treatment did not affect the in vitro and in vivo proliferation of MRSA, animal studies showed that it reduce catheter infection, highlighting the potential of this D-amino acid as a therapeutic agent. MORE

• Disruption of Enterococcus faecalis biofilms using individual and plasma polymer encapsulated D-amino acids.

Khider D, Rossi-Fedele G, Fitzsimmons T, Vasilev K, Zilm PS.
Clin Oral Investig. 2020 Nov 2. doi: 10.1007/s00784-020-03663-0. Epub ahead of print. PMID: 33140160.

In this work Khider and co-workers propose a methodology to produce plasma polymer encapsulated D-amino acids (PPEDAAs) and evaluate the potential of this technology to provide a sustained release of D-amino acids as well as the consequent ability to disassemble and prevent the formation of E. faecalis biofilms of PPEDAAs in root canals following obturation. The authors reported that the anti-biofilm activity of D-methionine, D-tryptophan, D-tyrosine and D-leucine remains unaltered upon encapsulation. Their results point to a future clinical application of this procedure. MORE

• A Mixture of D-Amino Acids Enhances the Biocidal Efficacy of CMIT/MIT Against Corrosive Vibrio harveyi Biofilm.

Liu X, Li Z, Fan Y, Lekbach Y, Song Y, Xu D, Zhang Z, Ding L, Wang F.
Front Microbiol. 2020 Sep 4;11:557435. doi: 10.3389/fmicb.2020.557435. PMID: 33013788; PMCID: PMC7498826.

The long-term use of biocide to control microbial contamination in the field of aviation fuel systems has raised concerns regarding their environmental impact and their role in fostering the onset of microbial drug resistance. The results of this study revealed that a triple combination treatment with a low dose of Chloro-2-Methyl-4-isothiazolin-3-one/2-Methyl-2H-isothiazole-3-one (CMIT/MIT, a broad spectrum biocide), D-tyrosine and D-methionine successfully prevented the establishment of the corrosive V. harveyi biofilm and effectively removed the mature biofilm. The observed synergistic effect allowed to propose the investigated D-amino acids mixture as a green and efficient biocide enhancer, paving the way for the development of D-amino acids mixtures with better biofilm dispersal ability and broader spectrum. MORE

• Antibacterial effect of high-purity nisin alone and in combination with D-amino acids or chlorhexidine in an endodontic-like biofilm model.

Pinheiro, E.T., Karygianni, L., Attin, T., Thurnheer, T. 
Antibiotics 2021, 10(2), 149; https://doi.org/10.3390/antibiotics10020149.

In order to identify new strategies to eradicate endodontic biofilms, here the effect of high-purity nisin alone and in combination with D-amino acids or chlorhexidine (CHX) was evaluated against an “endodontic-like” biofilm model. Nisin and D-AAs, alone or in combination, were not effective in reducing bacteria after short or long exposure times while combined treatment using nisin and CHX showed similar antibiofilm activity compared with the use of CHX alone. MORE

ANALYTICAL METHODS:

• Simultaneous Measurement of Amino Acid Enantiomers in Aged Mouse Brain Samples by LC/MS/MS Combined with Derivatization Using Nα-(5-Fluoro-2,4-dinitrophenyl)-L-leucinamide (l-FDLA).

Yamamoto T, Yaku K, Nakagawa T.
Metabolites. 2021 Jan 15;11(1):57. doi: 10.3390/metabo11010057. PMID: 33467775; PMCID: PMC7829926.

Considering their relevant physiological role in higher brain functions, D-amino acids (and the respective L-enantiomers) levels must be precisely measured in cells and tissues, ensuring high selectivity. Here, a novel quantification method based on Nα-(5-Fluoro-2,4-dinitrophenyl)-L-leucinamide (l-FDLA) as a derivatizing agent, followed by liquid chromatography–tandem mass spectrometry (LC/MS/MS) with a conventional reversed-phase column, has been used to evaluate the D-amino acids content in murine aged brain tissues. The proposed chromatographic method, allowed to separate most of the amino acids enantiomers and appeared more sensitive compared with other reported procedures (at least in the case of D-Ala and D-Asp). The authors confirmed previous findings reporting reduced levels of D-Ser and D-Asp in the hippocampus during aging and, notably, showed increased level of D-Phe in the thalamus. MORE

• A Miniaturized Enzymatic Biosensor for Detection of Sensory-Evoked D-serine Release in the Brain.

Siba Moussa, Marion R. Van Horn, Aryan Shah, Loredano Pollegioni, Christopher J. Thibodeaux, Edward S. Ruthazer and Janine Mauzeroll
Journal of The Electrochemical Society, 2021 Volume 168, Number 2.

In this work, a robust methodology for the fabrication of a reproducible miniaturized 10 μm D-serine detecting amperometric biosensor was developed. This biosensor is based on yeast D-amino acid oxidase immobilized on a poly-meta-phenylenediamine modified 10 μm Pt disk microelectrode. The biosensor shows a limit of detection of 0.361 μM, a high sensitivity (283 μA cm−2 mM−1) and was stable for over four hours of continuous use. Ex vivo D-serine measurements were made from Xenopus laevis tadpole brains: D-serine levels in the brain fluctuated with sensory experience. The biosensor was also used in vivo successfully. MORE

• Simultaneous Determination of Free DL-Amino Acids in Natto with Novel Fluorescent Derivatization by UPLC-F.

Jin, Y., Xu, CY., Wang, J., Xiaoxi Man, Qing Shi,  Fenghuan Nie, Jun Nan, Jun Zhe Min 
Food Anal. Methods (2021). https://doi.org/10.1007/s12161-020-01959-1.

A new simple and sensitive method for the simultaneous detection of free D,L-amino acids was established by UPLC-fluorescence using the fluorescence derivatization reagent DBD-trans-2-methyl-L-proline. The procedure is characterized by a detection limit of 0.25–2.5 pmol and a 86.65–118.70% average recovery. The method was applied to the simultaneous detection of D,L-Gln, D,L-Asp, D,L-Glu, and D,L-Ala detection in natto beans and mucus. MORE

ENZYMES ACTIVE ON D-AAs &  BIOTECHNOLOGICAL APPLICATIONS:

• Development of a Combination Fermentation Strategy to Simultaneously Increase Biomass and Enzyme Activity of D-amino Acid Oxidase Expressed in Escherichia coli.

Xu JM, Cao HT, Wang M, Ma BJ, Wang LY, Zhang K, Cheng F, Xue YP, Zheng YG.
Appl Biochem Biotechnol. 2021 Feb 4. doi: 10.1007/s12010-021-03519-7. Epub ahead of print. PMID: 33538962.

Here, a new and optimized high cell densities fermentation procedure for large scale production of the recombinant D-amino acid oxidase from the yeast Rhodotorula gracilis (RgDAAO) in E. coli is reported. The fermentation strategy, based on the coexpression of catalase (to prevent the toxic effect of increased cellular levels of H2O2), the addition of lactose and D-alanine (the latter important for the bacterial cell wall formation and which is depleted by the overexpressed enzyme) and on a controlled feeding mode, allows an 80% increase in biomass production and specific RgDAAO activity. Notably, the application of the recombinant enzyme to the purification of L-phosphinothricin, an herbicidal with a huge market demand, from racemic mixture containing the D-stereoisomer, is also proposed. MORE

• AtDAT1 Is a Key Enzyme of D-Amino Acid Stimulated Ethylene Production in Arabidopsis thaliana.

Suarez J, Hener C, Lehnhardt VA, Hummel S, Stahl M, Kolukisaoglu Ü. 
Front Plant Sci. 2019 Dec 12;10:1609. doi: 10.3389/fpls.2019.01609.

D-amino acids stimulate ethylene production in plants. Here, the Arabidopsis accession Landsberg erecta (Ler), defective in metabolizing D-AAs, was studied by combining genetics and molecular biology of T-DNA insertion lines together with biochemical and physiological approaches. AtDAT1 was identified as a major D-AA transaminase in Arabidopsis; the enzyme showed the highest activity on D-methionine. Germination of seedlings led to enhanced growth inhibition of atdat1 mutants on D-Met. Indeed, these mutants showed an increased D-AA stimulated ethylene production and an alteration of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). The specific effects of D-Met on ACC metabolism, ethylene production and plant development of dat1 mutants unraveled the impact of AtDAT1 on these processes and highlighted the influence of additional factors or processes, which await for additional studies. MORE

• D-Amino Acid Substituted Peptides as Potential Alternatives of Homochiral L-Configurations.

Shen, J.
Amino Acids, 2021 Feb;53(2):265-280. doi: 10.1007/s00726-021-02947-3.

This work concluded that some combinations of a mixture of L- and D-amino acids can potentially act as essential building blocks of life. At first, tripeptides composed of Asp, Ser, and Val showed that different positions made a difference in the minimal folding energy of peptides, while the chemical classification of amino acid did not. Then, hierarchical cluster analysis for dipeptides with all possible combinations of ten prebiotic amino acids (i.e. Gly, Ala, Asp, Glu, Ile, Leu, Pro, Ser, Thr, and Val) and their D-enantiomer substituted derivatives generated five clusters. Primordial simple polypeptides were modeled: peptides with α-helices, long β-sheets, and long loops were usually less sensitive to D-amino acid replacements than short β-sheets. Intriguingly, amongst 129 D-amino acid residues, mutation sensitivity profiles presented that the ratio of more to less stable residues was ~ 1. MORE

• Highly selective synthesis of D-amino acids via stereoinversion of corresponding counterpart by an in vivo cascade cell factory.

Zhang, D.-P., Jing, X.-R., Wu, L.-J., Fan, A.-W., Nie, Y.  Xu, Y. 
Microbial Cell Factories, Volume 20(1), December 2021, Article number 11.

In this work, an efficient in vivo biocatalysis system for the synthesis of D-amino acids from L-enantiomers was generated by co-expressing in recombinant Escherichia coli the membrane-associated enzyme L-amino acid deaminase from Proteus mirabilis (LAAD), meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum (DAPDH), and formate dehydrogenase from Burkholderia stabilis (FDH). Following the optimization of enzyme expression, the E. coli pET-21b-MBP-laad/pET-28a-dapdh-fdh whole-cell biocatalyst catalyzed the stereoinversion of 150 mM L-Phe into the D-enantiomer, with quantitative yields (> 99% ee) in 24 h, by the addition of 15 mM NADP+ and 300 mM ammonium formate. This biocatalyst was also used for the stereoinversion of various aromatic and aliphatic L-amino acids. MORE

• Enzyme cascade for biocatalytic deracemization of D,L-phosphinothricin.

Cao, C.-H., Gong, H., Dong, Y., Li, J.-M., Cheng, F., Xue, Y.-P., Zheng, Y.-G.
Journal of Biotechnology, Volume 325, 10 January 2021, Pages 372-379.

Deracemization of D,L-phosphinothricin (D,L-PPT) is a promising way to generate optically pure L-PPT. Here, a multi-enzyme redox cascade was developed for deracemization of PPT based on an oxidative reaction by D-amino acid oxidase (and a catalase for removing H2O2) and a reductive reaction by a glufosinate dehydrogenase (and a glucose dehydrogenase for cofactor regeneration). The inhibitory effect of glucose on the oxidative reaction was avoided using a “two stages in one-pot” strategy. L-PPT was obtained with a high yield (89 %) and > 99 % enantiomeric excess at substrate loading of 300 mM in absence of addition of extra NADP+. MORE

The D-amino acids International Research Center “DAAIR“ has been established in Gerenzano (Varese, Italy) in 2019 with the aim to support and perform scientific research projects and activities on the field of D-amino acids. The Center, located inside the Fondazione Istituto Insubrico Ricerca per la Vita, is aimed to represent a pole of excellence at international level for dissemination and research involving the D-amino acids (Director Silvia Sacchi).

The guiding principle is support the research projects aimed to investigate the involvement of D-amino acids in main physiological processes, from bacteria to humans. The ultimate goal is to actively participate to the elucidation of the mechanisms by which the D-amino acids perform specific functions, and to identify their presence and concentration in different organisms and compartments, also with regards to well-established functional states, with particular emphasis to pathological states. Understand the involvement of D-amino acids in important diseases as a way to set up novel therapeutic strategies.

Contacts: info@d-aminoacids.com;
director@d-aminoacids.com;
www.d-aminoacids.com