Newsletter 05/2022 edited by Loredano Pollegioni

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 PATHOLOGIES:

• Promising role of D-amino acids in irritable bowel syndrome 

Yuka Ikeda, Kurumi Taniguchi, Haruka Sawamura, Ai Tsuji, Satoru Matsuda
World J Gastroenterol., 2022; 28(31): 4471-4474. doi: 10.3748/wjg.v28.i31.4471. 

Alterations in the microbiota of the gut-brain axis may be linked to the pathophysiology of Irritable Bowel Syndrome (IBS). The gut microbiota can produce D-amino acids and their presence has been linked to the protection of several organs in the body. This work is focused to shed light on the roles of D-amino acids, which could be used for the treatment of IBS.

• Blood D-Amino Acid Oxidase Levels Increased With Cognitive Decline Among People With Mild Cognitive Impairment: A Two-Year Prospective Study

Chieh-Hsin Lin, Hsien-Yuan Lane
International Journal of Neuropsychopharmacology, 2022, 25(8), 660–665. https://doi.org/10.1093/ijnp/pyac027.

Dysregulation of N-methyl-D-aspartate receptor (NMDAR) neurotransmission is related to the pathogenesis of Alzheimer’s disease (AD) and the enzyme D-amino acid oxidase (DAAO), by controlling D-serine concentration, regulates NMDAR function. A cross-section study found that DAAO levels in serum positively correlated with the severity of cognitive aging among elderly individuals. Here, a 2-year prospective study explored the role of DAAO levels in predicting the outcome of patients with mild cognitive impairment (MCI). From baseline to endpoint (24 months), serum DAAO levels increased significantly, and cognitive ability declined in the MCI patients. An increase in DAAO levels was also apparent in healthy controls but AD assessment scale-cognitive subscale scores did not significantly change. The DAAO levels at months 12 and 18 were considered predictive of cognitive impairment among the MCI patients.

• Serine racemase interaction with N-methyl-D-aspartate receptors antagonist reveals potential alternative target of chronic pain treatment: Molecular docking study

Laksono RM, Kalim H, Rohman MS, Widodo N, Ahmad MR. 
J Adv Pharm Technol Res., 2022;13(3):232-237. doi: 10.4103/japtr.japtr_72_22.

This study investigated N-methyl-D-aspartate receptor (NMDAR) antagonist interactions with serine racemase (SR) to obtain potential chronic pain target therapy. Several NMDAR antagonist drugs were obtained from the drug bank, and malonate was used as a control inhibitor. These studies showed that several NMDAR antagonists – such as haloperidol, halothane, ethanol, and tramadol – bind to SR in the specific binding site.

• D-Amino Acids and Classical Neurotransmitters in Healthy and Type 2 Diabetes-Affected Human Pancreatic Islets of Langerhans

Lee CJ, Schnieders JH, Rubakhin SS, Patel AV, Liu C, Naji A, Sweedler JV.
Metabolites, 2022;12(9):799. doi: 10.3390/metabo12090799.

In this work, the signaling molecules D-serine (D-Ser) and D-aspartate (D-Asp), along with multiple classical neurotransmitters and related molecules, were studied in healthy versus type 2 diabetes-affected human islets using capillary electrophoresis separations. Significantly reduced D-Ser percentage and GABA levels were found in type 2 diabetes-affected islets compared to healthy islets. The negative correlations of many of the investigated signaling molecules – such as D-Ser percentage, D-Asp, serotonin, and GABA levels – with hemoglobin A1c levels and thus with the progression of type 2 diabetes further demonstrate the disruption in intra- or inter-islet signaling pathways: the results suggest these cell-to-cell signaling molecules as potential therapeutic targets.

• D-Amino Acids as Novel Blood-based Biomarkers

Murtas G, Pollegioni L. 
Curr Med Chem., 2022, 29(24):4202-4215. doi: 10.2174/0929867328666211125092438.

D-amino acids are present in the human body originating from diet, bacterial flora, and endogenous synthesis (at least for D-serine and, probably, D-aspartate). D-amino acids are involved in important physiological processes (e.g., D-serine and D-aspartate act on the N-methyl-D-aspartate receptor as co-agonist and agonist, respectively) and increasing evidence links D-amino acids to different pathological states. This review is focused on the determination of blood levels of D-amino acids as diagnostic and prognostic biomarkers. The experimental evidence suggests investigating their levels in several pathologies, from neurodegenerative diseases to diabetes mellitus. The authors concluded that further studies are required to standardize/automatize the determinations and for confirming their clinical effectiveness.

• Unveiling the Bio-corona Fingerprinting of Potential Anticancer Carbon Nanotubes Coupled with D-Amino Acid Oxidase

Boreggio, M., Rosini, E., Gambarotti, C., Pollegioni L., Fasoli E
Mol Biotechnol., 2022, 64, 1164–1176. https://doi.org/10.1007/s12033-022-00488-y.

An anticancer oxidation therapy (based on the controlled production of ROS directly into the tumor site) based on yeast D-amino acid oxidase (DAAO) that produces hydrogen peroxide from D-amino acids, was developed by adsorbing the enzyme onto multi-walled carbon nanotubes (MWCNTs), previously functionalized with polylactic-co-glycolic acid (PLGA) or polyethylene glycol (PEG) at different degrees to reduce their toxicity and to be targeted directly into the tumor. DAAO-functionalized nanotubes (f-MWCNTs) induced toxic effects to selected tumor cell lines. After incubation in human plasma, the protein corona was investigated by SDS-PAGE and MS analysis. The results showed that the PEGylated MWCNTs at low degree are the most biocompatible nanocarrier for adsorbed DAAO, preserving its anticancer activity and forming a bio-corona able to reduce both defensive responses and blood clearance.

• D-Tryptophan suppresses enteric pathogen and pathobionts and prevents colitis by modulating microbial tryptophan metabolism

Natsumi Seki, Tatsuki Kimizuka, Monica Gondo, Genki Yamaguchi, Yuki Sugiura, Masahiro Akiyama, Kyosuke Yakabe, Jun Uchiyama, Seiichiro Higashi, Takeshi Haneda, Makoto Suematsu, Koji Hase, Yun-Gi Kim
iScience, 2022, 25(8), 104838. https://doi.org/10.1016/j.isci.2022.104838

D-AAs are produced by gut microbiota and can act as potent bactericidal molecules and regulate the ecological niche of the intestine. Here, D-tryptophan (D-Trp) was shown to inhibit the growth of enteric pathogen and colitogenic pathobionts, to protect mice from lethal C. rodentium infection via reduction of the pathogen, to prevent the development of experimental colitis by the depletion of specific microbes in the intestine, and to increase the indole acrylic acid concentration.

• New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture

Saeed Niazi Vahdati, Hossein Behboudi, Sepideh Aliniaye Navasatli, Sara Tavakoli, Maliheh Safavi,
Microbiological Research, 2022, 263, 127107. https://doi.org/10.1016/j.micres.2022.127107

Many bacteria produce and release D-amino acids to inhibit biofilm formation. This review focuses on the role of D-amino acids in controlling several bacterial biofilms and on the mechanisms involved in this process.

• Regulation of L- and D-Aspartate Transport and Metabolism in Acinetobacter baylyi ADP1

Stacy R. Bedore, Alicia L. Schmidt, Lauren E. Slarks, Chantel V. Duscent-Maitland, Kathryn T. Elliott, Silke Andresen, Flavia G. Costa, R. Sophia Weerth, Melissa P. Tumen-Velasquez, Lindsey N. Nilsen, Cassandra E. Dean, Anna C. Karls, Timothy R. Hoover, Ellen L. Neidle
Applied Environmental Microbiology, 2022, 88(15). https://doi.org/10.1128/aem.00883-22

The bacteria Acinetobacter baylyi ADP1 can use both D-Asp and L-Asp as the sole carbon or nitrogen source. Two LysR-type transcriptional regulators (LTTRs), DarR and AalR, control D- and L-Asp metabolism in strain ADP1: the heterologous expression of A. baylyi proteins enabled E. coli to use D-Asp as the carbon source when either of two transporters (AspT or AspY) and a racemase (RacD) were coexpressed. A third transporter, designated AspS, was also discovered to transport Asp in ADP1. ADP1 consumed L- and D-Asn and L-Glu, but not D-Glu, as the sole carbon or nitrogen source using interrelated pathways.

• Mycobacterium tuberculosis survival and biofilm formation studies: effect of D-amino acids, D-cycloserine and its components

Ram Kumar, Nirbhay Singh, Anu Chauhan, Mukesh Kumar, Rabi Sankar Bhatta, Sudheer Kumar Singh
J Antibiot., 2022, 75, 472–479. https://doi.org/10.1038/s41429-022-00534-6

Mycobacterium tuberculosis D-amino acid oxidase deletion led to reduced biofilm-forming ability. Here, selected D-amino acids were used to study their role in the prevention of biofilm formation and to understand whether D-cycloserine’s activity was due to presence of D-serine. D-serine (as well as D-cycloserine) limits biofilm formation in Mycobacterium tuberculosis H37Ra (Mtb-Ra), but it shows no effect on pre-formed biofilm (while D-cycloserine disrupts existing biofilm). D-alanine, D-valine, D-phenylalanine, D-serine, and D-threonine had no disruptive effect on pre-formed biofilm of Mtb-Ra, either individually or in combination.

D-AAs AND BIOTECHNOLOGY:

• PET Imaging of Active Invasive Fungal Infections with D-[5-11C]-Glutamine

Cynthia M. Co, Aditi Mulgaonkar, Ning Zhou, Shelby Harris, Orhan K. Öz, Liping Tang, Xiankai Sun
ACS Infect. Dis., 2022, 8(8), 1663–1673. https://doi.org/10.1021/acsinfecdis.2c00249

The increasing prevalence and severity of invasive fungal infections (IFIs) asks for rapid diagnosis of fungal pathogens. On this side, radiotracers derived from D-amino acids (DAAs) show promise as bacterial-specific positron emission tomography (PET) imaging agents due to their preferential consumption by bacteria and largely nonutilization by hosts. Using D-[5-11C]-Gln, the authors highlighted the translational potential of this molecule for noninvasive PET imaging of IFIs.

ENZYMES ACTIVE ON D-AAs:

• Molecular basis and functional development of enzymes related to amino acid metabolism

Tohru Yoshimura
Bioscience, Biotechnology, and Biochemistry, 2022, 86(9), 1161–1172. https://doi.org/10.1093/bbb/zbac102

This interesting review reports on the reaction mechanism of various pyridoxal enzymes especially related to D-amino acids metabolism, whose roles in mammals have recently attracted attention.

• LD-transpeptidases: the great unknown among the peptidoglycan cross-linkers

Alena Aliashkevich, Felipe Cava
FEBS Journal, 2022, 289(16), 4718-4730. https://doi.org/10.1111/febs.16066

The peptidoglycan (PG) cell wall is essential for the shape and viability of bacteria: PG-cross-linking enzymes like the penicillin-binding proteins are among the best targets for antibiotics. On this side, LD-transpeptidases (LDTs) seemed to contribute less to PG synthesis and, thus, were less investigated. In recent years, LDTs were associated with cell wall adaptation to stress including β-lactam antibiotics, outer membrane stability, and toxin delivery. Furthermore, LDTs were proposed as the main synthetic PG-transpeptidases in some bacteria. This review is aimed to shed light on this intriguing topic.

• The Stability of Dimeric D-amino Acid Oxidase from Porcine Kidney Strongly Depends on the Buffer Nature and Concentration

Diego Carballares, Javier Rocha-Martin, Roberto Fernandez-Lafuente 
Catalysts, 2022, 12(9), 1009. https://doi.org/10.3390/catal12091009

The first step of the inactivation of the enzyme D-amino acid oxidase (DAAO) from porcine kidney differs with pH: at pH 5 and 7 it is the enzyme subunit dissociation, while at pH 9 FAD dissociation also plays a relevant role. The effect of the buffer nature and concentration on enzyme stability was investigated. The observed effects were usually more significant when using low concentrations of DAAO and were not reverted upon adding exogenous FAD. However, when using an immobilized DAAO biocatalyst which presented enzyme subunits attached to the support (thus dissociation was unfeasible), the effect of buffer composition on enzyme stability almost disappeared.

D-AAs IN PEPTIDES:

• Biotinylated peptides substituted with D-amino acids with high stability as anti-anaphylactic agents targeting platelet-activating factor

Akira Sato, Takahiro Fukase, Keiichi Ebina
Journal Peptide Science, 2022, 28(19), e3412. https://doi.org/10.1002/psc.3412

Platelet-activating factor is an important lipid mediator of anaphylaxis and an anti-anaphylactic agent target. This work focuses on the anti-anaphylactic effects of three biotinylated heptapeptides containing D-amino acids. The results suggest that two of them may show systemic and local inhibitory effects as anti-anaphylactic agents targeting PAF.

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