Newsletter 01/2023 edited by Loredano Pollegioni

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

• Endogenous D-serine exists in the mammalian brain independent of synthesis by serine racemase

Osaki, Akina; Aoyama, Marie; Mita, Masashi; Hamase, Kenji; Yasui, Masato; Sasabe, Jumpei
Biochemical and Biophysical Research Communications, 641, 186-191, 2023, DOI 10.1016/j.bbrc.2022.12.037

This work focused on the origin of brain D-serine in mice. While elimination of serine racemase (SR) significantly reduced D-Ser in the cerebral cortex, a significant amount of this D-amino acid remained in both neonates and adults. Notably, in germ-free mice the levels of D-Ser were not different in the cerebral cortex, while treatment of SR-KO mice with antibiotics yielded a significant reduction of intestinal but no brain D-Ser. Restriction of dietary intake reduced systemic D-Ser level, as well as its level in the cerebral cortex, but did not account for brain D-Ser found in the SR-KO mice. The authors showed that endogenous D-Ser in the brain also arises from a way different from SR.

• Racemization rate and biomolecular characterization of D-serine synthesizing bacteria Bacillus tequilensis A1C1
  Shikha Kapil, Monika Bhattu, Vipasha Sharma, Tarun Kumar
  Lett Appl Microbiol., 2023, 76(1), ovac017, doi: 10.1093/lambio/ovac017.

D-Serine is present in various prokaryotes and eukaryotes: in plants, it has a role in the nitrogen cycle regulation and pollen tube growth. In this work, bacteria were isolated from soil samples from different places in North India for D-Ser synthesis ability. Bacterial isolate A1C1 with maximum D-Ser synthesis (0.919 ± 0.02 nM, under optimal growth conditions) was identified as Bacillus tequilensis based on 16S RNA sequencing. 

D-AAs AND PATHOLOGIES:

• Ultrapure and potent tannic acid (UPPTA) is a novel inhibitor of D-amino acid oxidase to improve the N-methyl-D-aspartate function of CNS disorders
  Mao, Yi-Wen; Lu, Lu-Ping; Shih, Po-Chang; Hsiao, Jui-Fu; Wu, Vivian; Tsai, Guochuan E.
  Phytomedicine Plus 3(1), 2023, Art. 100399, DOI 10.1016/j.phyplu.2022.100399

 Tannic acids (TAs) have been used as a traditional Chinese medicine for millennia. Here, a number of galloyl moieties was positively correlated with the inhibitory potency of D-amino acid oxidase (DAAO). In vivo studies using MK-801 treated mice showed that the ultrapure and potent tannic acid (UPPTA) improved the N-methyl-D-aspartate-hypofunction-induced hyperactivity, working memory, and sensory motor gating deficits, suggesting its potential as a novel therapeutic candidate for treating CNS disorders through DAAO inhibition.

• Involvement of DAAO Overexpression in Delayed Hippocampal Neuronal Death
  Liu, Hao; Zhang, Jun-Tao; Mou, Chen-Ye; Hao, Yue; Cui, Wei
  Cells, 11(22), 2022, Art. 3689, DOI 10.3390/cells11223689

This study investigated the pathological increment of hippocampal D-amino acid oxidase (DAAO) and its potential relationship with delayed hippocampal neuronal death in Ischemia–reperfusion induced in mice through middle cerebral artery occlusion (MCAO). Hippocampal astrocytic DAAO was strikingly increased following ischemic stroke, with the maximum at day 5 after surgery, followed by the manifestation of neurobehavioral deficits. Astrocytic DAAO was mainly expressed in the hippocampal CA2 region and was linked with subsequent neural apoptosis, thus contributing to neuronal death. The use of a DAAO inhibitor relieved behavioral status and delayed hippocampal neuronal death. Furthermore, in transfected primary astrocytes, DAAO overexpression inhibits cell activity, induces cytotoxicity, and promotes hippocampal neuronal death at least partly by enhancing H2O2 levels with subsequent activation of TRP calcium channels in neurons. The authors concluded that increased hippocampal DAAO is associated with the development of delayed neuronal death after MCAO onset via astrocyte–neuron interactions: DAAO seems a promising therapeutic target for the treatment of neurological disorders.

• Increased levels of oral Streptococcus-derived D-alanine in patients with chronic kidney disease and diabetes mellitus
  Nakade, Yusuke; Iwata, Yasunori; Sakai, Norihiko; Mita, Masashi; Nakane, Maiko; Hamase, Kenji; Suda, Wataru; Toyama, Tadashi; Kitajima, Shinji; Hara, Akinori; Shimizu, Miho; Ogushi, Chikako
  Scientific Reports, 12(1), 2022, Art. 21773, DOI 10.1038/s41598-022-26175-1

This work studied the D-amino acid (AA) profiles, and associated bacteria, in patients with chronic kidney disease (CKD), with and without diabetes mellitus (DM). On 12 healthy controls and 54 patients the salivary, stool, plasma, and urine chiral AA levels were determined by two-dimensional HPLC. 16S rRNA gene sequencing analysis of the oral and gut microbiota was used to determine the abundance of bacterial species. Plasma levels of D-Ala and D-Ser increased in patients with CKD compared to healthy adults, and plasma D-Ala levels were higher in patients with CKD and DM than in those without DM. The salivary Streptococcus level increased in patients with CKD and DM and positively correlated with plasma D-Ala levels. Patients with CKD and DM had unique oral microbiota and D-Ala profiles, and thus D-Ala level was proposed as a potential biomarker.

• Antimicrobial activity of D-amino acid in combination with photo-sonoactivated hypericin nanoparticles against Acinetobacter baumannii
  Maryam Pourhajibagher, Nava Hosseini, Abbas Bahador
  BMC Microbiol, 2023, 23(1):23, doi: 10.1186/s12866-023-02758-4.

To treat the emergence of the multidrug-resistant Acinetobacter baumannii strains, the antimicrobial photo-sonodynamic therapy (aPSDT) using hypericin nanoparticles (HypNP) in combination with D-Tryptophan (D-Trp) was investigated. A synergistic activity in the combination of HypNP and D-Trp against A. baumannii was observed, as well as a significant biofilm degradation effect. The authors concluded that HypNP@D-Trp-mediated aPSDT can be considered a promising strategy to overcome the infections caused by A. baumannii.

D-AAs AND BIOTECHNOLOGY:

• Investigation of D-Amino Acid-Based Surfactants and Nanocomposites with Gold and Silica Nanoparticles as against Multidrug-Resistant Bacteria Agents
  Shim, Jae Ho, Gwak, Sungduk; Ahn, Byung Kook; Han, Hogyu; Hong, Yeonsun; Shin, Ok Sarah
  ACS Omega, 7(50), 46146-46155, 2022, DOI 10.1021/acsomega.2c04220

In this work, D-amino acid-based surfactants (D-AASs) were synthesized and their antimicrobial activity was evaluated. N-α-lauroyl-D-Arg ethyl ester hydrochloride (D-LAE), D-Pro dodecyl ester (D-PD), and D-Ala dodecyl ester (D-AD) showed antibacterial activity against both Gram-positive and -negative bacteria. For improving their antibacterial properties by eliminating drug-resistant pathogens, D-LAE was coated on gold (AuNP) and silica (SiNP) nanoparticles and showed antibacterial activity higher than that of D-LAE alone. D-PD has enhanced antibacterial activity upon being coated on AuNP only.

• Ribosomal incorporation of negatively charged D-α- and N-methyl-L-α-amino acids enhanced by EF-Sep

Katoh, Takayuki; Suga, Hiroaki
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 378(1871), 2022003827, 2023, DOI 10.1098/rstb.2022.0038

Ribosomal incorporation of D-amino acids (D-AA) and N-methyl-L-amino acids (MeAA) with negatively charged sidechains into nascent peptides is quite inefficient compared to neutral or positively charged ones. This is because of the low binding affinity of their tRNA to elongation factor-thermo unstable (EF-Tu). The amino acid binding pocket of EF-Tu bearing Glu and Asp causes electric repulsion against the negatively charged amino acid charged on tRNA. Here, two strategies were evaluated: (i) use of an EF-Tu variant, called EF-Sep, in which the Glu216 and Asp217 residues in EF-Tu are substituted with Asn216 and Gly217, respectively; and (ii) improvement of the T-stem affinity using an artificially developed chimeric tRNA, whose T-stem is derived from Escherichia coli tRNAGlu that shows high affinity to EF-Tu. The incorporation efficiency of D-Asp, D-Glu, MeAsp and MeGlu was increased, this allowing ribosomal synthesis of macrocyclic peptides containing multiple D-Asp or MeAsp.

• Asymmetric Synthesis of Enantiomerically Pure Aliphatic and Aromatic D-Amino Acids Catalyzed by Transaminase from Haliscomenobacter hydrossis
  Bakunova, Alina K.; Isaikina, Tatiana Y.; Popov, Vladimir O.; Bezsudnova, Ekaterina Yu
  Catalysts, 12(12), 2022, Art. 1551, DOI 10.3390/catal12121551

This work focused on the use of the PLP-dependent D-amino acid transaminase (DAAT) from Haliscomenobacter hydrossis for the enzymatic asymmetric synthesis of optically pure aliphatic and aromatic D-amino acids using D-Glu as a source of the amino group. A one-pot three-enzyme system (including the transaminase, hydroxyglutarate dehydrogenase, and glucose dehydrogenase) produced D-amino acids with a product yield of 95–99% and an enantiomeric excess > 99%. Notably, a high concentration of α-keto acids and a low reaction temperature (30 °C) can reduce the cofactor leakage under reaction conditions

ENZYMES ACTIVE ON D-AAs: 

• Engineering the Thermostability of a D-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of D-Tryptophan
  Jiamin Hu, Xiaoyu Chen, Lu Zhang, Jieyu Zhou, Guochao Xu, Ye Ni
  J Agric Food Chem., 2023, 71(1), 660-670, doi: 10.1021/acs.jafc.2c07781

The use of ancestral sequence reconstruction and consensus sequence analysis coupled to engineered through greedy-oriented iterative combinatorial mutagenesis allowed to increase the thermostability of a novel D-carbamoylase derived from Nitratireductor indicus (NiHyuC). The S202P/E208D/R277L (M4Th3) variant showed significantly elevated thermostability. This enzyme variant catalyzed the conversion of 10 mM N-carbamoyl-D-tryptophan into D-Trp, with a 96.4% conversion ratio after 12 h. Molecular dynamics simulation revealed details related to the substitutions introduced. This thermostable D-carbamoylase is useful in the hydantoinase process aimed at industrial synthesis of optically pure natural and non-natural amino acids.

• Mechanistic aspects of the transamination reactions catalyzed by D-amino acid transaminase from Haliscomenobacter hydrossis
  Bakunova, Alina K.; Kostyukov, Alexey A.; Kuzmin, Vladimir A.; Popov, Vladimir O.; Bezsudnova, Ekaterina Yu
  Biochimica et Biophysica Acta – Proteins and Proteomics, 1871(21), 2023, Art. 140886, DOI 10.1016/j.bbapap.2022.140886

PLP-dependent D-amino acid transaminases (DAATs) catalyze stereoselective reversible transfer of the amino group between D-amino acids and keto acids. DAATs are known to synthesize D-Glu for cell wall peptidoglycans. Here, the pre-steady-state kinetics of the half-reactions of DAAT from Haliscomenobacter hydrossis with D-Glu, D-Ala, D-Leu, and D-Phe was studied using a stopped-flow technique. Kinetics with D-Leu and D-Phe revealed the increase in the rates of deamination of these substrates in the overall transamination reaction with α-ketoglutarate. The study contributed to quantify the specificity of H. hydrossis DAAT with different D-amino acids.

• Immobilization-stabilization of the dimeric D-amino acid oxidase from porcine kidney
  Carballares, Diego; Fernandez-Lafuente, Roberto; Rocha-Martin, Javier
  Process Biochemistry, 122, 120-128, 2022, DOI 10.1016/j.procbio.2022.10.002

This paper reports a deep investigation of the immobilization of the dimeric D-amino acid oxidase (DAAO) with different methodologies. Considering all factors, immobilization on glutaraldehyde support at pH 7 seems the best immobilization protocol for DAAO.

D-AAs IN PEPTIDES: 

• Effect of Mini-PEGs Modification on the Enzymatic Digestion of D-Amino Acid-Containing Peptides under the Action of PROK
  Liang Yan, Yongqi Ke, Yu Wang, Jingkui Yang, Yujian He, Li Wu
  Chemistry, 2022, doi: 10.1002/chem.202203524, Online ahead of print

This study focused on the influence of mini-PEGs modification on enzymatic hydrolysis ability of D-amino acid-containing peptides (DAACP), concluding that PEGylation promoted enzymatic hydrolysis of the DAACP. The analysis of the enzymatic cleavage sites demonstrated a similar cleavage pattern of the PEGylated DAACP to that of the unmodified peptide. The computational simulations further showed that the enhanced enzymatic hydrolysis ability can be attributed to the strong interaction between proteinase K and the peptide after PEG3 modification and the resulting formation of a mature catalytic triad structure.

D-AAs AND ANALYTICAL METHODS:

• Characterization of D-amino acids in colostral, transitional, and mature preterm human milk
  Sol Maiam Rivera Velez, Melanie Newkirk, Aurelie Roux, Greg Ellis, Robert Harlan, Mitzi Donabel Ang Go, Prabhu Satya Parimi, David Graham
  Amino Acids, 2022, doi: 10.1007/s00726-022-03204-x. Online ahead of print

This work set up a fast method for simultaneous analysis of amino acid enantiomers in human milk using liquid chromatography with tandem mass spectrometry: a total of 41 amino acids were separated without chemical derivatization. The human milk from mothers of preterm infants contains concentrations of D-amino acids that range from 0.5 to 45% that of the L-amino acids and the level of most D-amino acids decreases as the milk production matures. The Holder pasteurization of milk does not cause racemization of L-amino acids. 

• Upconversion NaYF4:Yb/Er-TiO2-Ti3C2Heterostructure-Based Near-Infrared Light-Driven Photoelectrochemical Biosensor for Highly Sensitive and Selective D-Serine Detection
  Huang, Likun; Liang, Zhishan; Zhang, Fang; Luo, Hui; Liang, Ruilian; Han, Fangjie; Wu, Zhifang; Han, Dongxue; Shen, Jun; Niu, Li
  Analytical Chemistry, 94(46), 16246-16253, 2022, DOI 10.1021/acs.analchem.2c04101

A near-infrared (NIR) light-driven NaYF4:Yb/Er-TiO2-Ti3C2 (NYF-TiO2-Ti3C2) heterostructure-based photoelectrochemical (PEC) biosensing platform was set up for D-Ser detection using D-amino acid oxidase (DAAO), which converts D-Ser into hydroxypyruvate and H2O2. The TiO2-Ti3C2 semiconductor and NaYF4:Yb/Er optical transducer formed a Schottky junction that provided an irreversible channel for electron transfer. Infrared light was converted into absorbable multiemission light, thereby effectively increasing light absorption. Simultaneously, the generated H2O2 rapidly scavenged photogenerated holes to separate electron-hole pairs, which amplified the photocurrent signal. Under optimal conditions, the NIR light-driven PEC biosensor exhibited an excellent performance for D-Ser detection (linear range of 2-1650 μmol/L and detection limit of 0.286 μmol/L). This system was used for analyzing human serum and rat cerebrospinal fluid specimens.

• A sensitive and economical method for simultaneous determination of D/L-amino acids profile in foods by HPLC-UV: Application in fermented and unfermented foods discrimination
  Gao, Li; Xu, Piao; Ren, Jiaoyan
  Food Chemistry, 4101, 2023, Art. 135382, DOI 10.1016/j.foodchem.2022.135382

This work described a sensitive and economical HPLC-UV method with FDAA derivatization to simultaneously detect 36 D,L-amino acids, with higher sensitivity and lower cost than other HPLC-based methods. Its linearity range (8–1000 µmol/L), limits of detection (2.68–62.44 pmol/L), limits of quantification (2.93 to 208.13 pmol/L), intraday precision (0.30−5.31%), interday precision (1.96−8.04%) and accuracy (86.53−121.46%) were significant parameters. This method was used in the determination of D,L-amino acids abundance in fermented and unfermented food materials, allowing the discrimination of food materials.

• Detection of Gastric Cancer-Associated D-Amino Acids and Carcinoembryonic Antigen by Colorimetric and Immuno ECL Sensing Platform Based on the Catalysis of N/S-Doped Carbon Dots @ N-Rich Porous Carbon Nanoenzyme
  Tang, Yun; Chen, Yanran; Liu, Yiwei; Xia, Yide; Zhao, Faqiong; Zeng, Baizhao
  Analytical Chemistry, 94(51), 17787-17794, 2022, DOI 10.1021/acs.analchem.2c03433

In this work, to improve the detection reliability, a dual-mode detection strategy for the detection of two biomarkers associated with gastric cancer was developed. In details, an N- and S-doped carbon dots-N-rich porous carbon nanoenzyme (N/S-CDs@NC) was prepared by a two-step pyrolysis of thiourea-penetrated zinc-based zeolite imidazole framework. It was then combined with the 3,3′,5,5′-tetramethylbenzidine-H2O2 system for the colorimetric detection of D-Pro and D-Ala in saliva, based on the reaction of D-amino acid oxidase to produce H2O2. The lower detection limits of D-Pro and D-Ala were 0.14 and 0.35 μM, respectively.

• A Novel Stereospecific Bioluminescent Assay for Detection of Endogenous D-Cysteine

Roychaudhuri, Robin; Gadalla, Moataz M.; West, Timothy; Snyder, Solomon H.
ACS Chemical Neuroscience, 13(23), 3257-3262, 2022, DOI 10.1021/acschemneuro.2c00528

This work used a novel, stereospecific, bioluminescent assay to identify endogenous D-Cys in substantial amounts in the eye, brain, and pancreas of mice. D-Cys is enriched in mice embryonic brains at day E9.5 (4.5 mM) and decreases progressively with development. D-Cys is also present in significantly amounts in the human brain white matter compared with gray matter. The novel luciferase-based assay, in which D-Cys is conjugated with cyano hydroxy benzothiazole, is stereospecific and allows the quantitative estimation of endogenous D-Cys in tissues. The bioluminescent in vivo imaging of D-Cys, a noninvasive detection method, will allow elucidating its function.

• Separation of the enantiomers of underivatized amino acids by using serially connected dual column high-performance liquid chromatography-tandem mass spectrometry
  Öztepe, Tuğçe; Kale, Nermin Büşra; Reçber, Tuba; Baysal, İpek; Yabanoğlu-Çiftçi, Samiye; Gumustas, Mehmet; Kır, Sedef; Chankvetadze, Bezhan; Nemutlu, Emirhan
  Journal of Chromatography A, 16838, 2022, Art. 463529, DOI 10.1016/j.chroma.2022.463529

A serially connected dual column liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is described here for the simultaneous separation and enantio.separation of proteinogenic amino acids. The best enantio-separation was achieved with a combination of zwitterionic and crown ether stationary phases using a gradient of two mobile phases. This method provided simultaneous enantio-separation of all proteinogenic amino acids, including isomeric and isobaric ones except for proline. The method was used to human lung adenocarcinoma cells (A549) and healthy human lung epithelial cells (BEAS-2B) cultivated with D-amino acid containing cocktails in order to evaluate D-amino acids transfer rate in normal and cancer cell lines. The D/L-amino acid ratios were different in cancer and normal cell lines for aspartic acid, cysteine, methionine, phenylalanine, and serine. 

• NMR Discrimination of D- and L-α-Amino Acids at Submicromolar Concentration via Parahydrogen-Induced Hyperpolarization
  Lennart Dreisewerd, Ruud L. E. G. Aspers, Martin C. Feiters, Floris P. J. T. Rutjes, Marco Tessari
  J. Am. Chem. Soc. 2023, XXXX, 2023, doi.org/10.1021/jacs.2c11285

The discrimination and quantification of D- and L-amino acids generally requires extensive sample manipulation resulting in high time costs and potential biases in the quantitative determination. Here, an approach based on the combination of non-hydrogenative parahydrogen-induced hyperpolarization and nuclear magnetic resonance was developed that allows detection, discrimination, and quantification of both D- and L-amino acids in complex mixtures such as biofluids and food extracts down to submicromolar concentrations. This method can be directly applied to the system under investigation without any prior isolation, fractionation, or functionalization step.

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