Newsletter 04/2024 edited by Loredano Pollegioni

The website of IDAR2024 is open now, please visit the following to have an update about the scientific programme:

http://soyaku.phar.kyushu-u.ac.jp/IDAR2024/

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.

04/2024

D-AAs AND PATHOLOGIES:

Urinary D-amino acid profiles in cats with chronic kidney disease

Kimura R, Ueda R, Tsujimura H, Ban T, Tanaka A. J Vet Med Sci. 2024 Jun 7. doi: 10.1292/jvms.24-0023. Online ahead of print. Chronic kidney disease (CKD) is highly prevalent in domestic cats. This study compared urinary D-amino acid levels between control and CKD-afflicted cats as a novel noninvasive method for assessing CKD. The urinary Dand L-amino acid levels of the cats were determined by chiral tandem liquid chromatography-tandem mass spectrometry. The CKD group had considerably lower urinary D-amino acid concentrations and enantiomeric ratios than the control group. The total urinary D-amino acid contents significantly correlated with blood parameters (creatinine and urea nitrogen).

Plasma D-asparagine and the D/L-serine ratio reflect chronic kidney diseases in children regardless of physique

Morishita T, Nishizaki N, Taniguchi S, Sakai S, Kimura T, Mita M, Nakagawa M, Endo A, Ohtomo Y, Yasui M, Shimizu T, Sasabe J Amino Acids. 2024 Jun 6;56(1):38. doi: 10.1007/s00726-024-03400-x. Biomarkers that accurately reflect renal function are essential in management of chronic kidney diseases (CKD). Here, a prospective study of children 2 to 18 years old with and without CKD was carried out by investigating the association of serine/asparagine enantiomers in body fluids with major biochemical parameters as well as physique. Plasma D-Asn and the D/L-Ser ratio had robust, positive linear association with serum creatinine and cystatin C, and detected CKD with high sensitivity and specificity, uninfluenced by body size or biochemical parameters. Furthermore, juvenile mice with uninephrectomy, ischemic reperfusion injury, or dexamethasone treatment were generated: kidney dysfunction increased plasma D-AAs and the D/L-Ser ratio, but dexamethasone treatment did not. Thus, plasma D-Asn and the D/L-Ser ratio can be useful markers for renal function in children.

L-serine deficiency: on the properties of the Asn133Ser variant of human phosphoserine phosphatase

Pollegioni L., Campanini B., Good J.-M., Motta Z., Murtas G., Buoli Comani V., Pavlidou D.-C., Mercier N., Mittaz-Crettol L., Sacchi S., Marchesani F. (2024) Scientific Reports, 14 (1), art. no. 12463. DOI: 10.1038/s41598-024-63164-y The phosphorylated pathway (PP) is made by three enzymes proposed to generate a reversible metabolon named the “serinosome”. Phosphoserine phosphatase (PSP) catalyses the last and irreversible step, representing the driving force pushing L-Ser synthesis, from which D-Ser is generated. Genetic defects of the PP enzymes result in strong neurological phenotypes. Here, the homozygous missense variant Asn133Ser PSP was identified in two siblings with a neurodevelopmental syndrome and a myelopathy. The recombinant variant enzyme does not show significant alterations in protein conformation and dimeric oligomerization state, as well as in enzymatic activity and functionality of the reconstructed PP. However, it is less stable than wild-type PSP. In patients’ fibroblasts a strong decrease in the level of the enzymes of the PP, a partial nuclear and perinuclear localization of variant PSP and a stronger perinuclear aggregates formation is apparent. The authors propose that these alterations contribute to the formation of a dysfunctional serinosome and thus to the observed reduction of LSer, glycine and D-Ser levels (the latter playing a crucial role in modulating NMDA receptors).

Serum dysregulation of serine and glycine metabolism as predictive biomarker for cognitive decline in frail elderly subjects

Imarisio A., Yahyavi I., Gasparri C., Hassan A., Avenali M., Di Maio A., Buongarzone G., Galandra C., Picascia M., Filosa A., Monti M.C., Pacchetti C., Errico F., Rondanelli M., Usiello A., Valente E.M. Translational Psychiatry. 2024. 14 (1), art. no. 281. DOI: 10.1038/s41398-024-02991-z Frailty is a common age-related clinical syndrome characterized by a decline in the function of multiple organ systems, increased vulnerability to stressors, and a huge socio-economic burden. Cognitive decline represents a critical domain of frailty associated with higher risk of adverse health outcomes. In this work, serum L-Glu, L-Gln, L-Asn, L-Asp, Gly, L-Ser and D-Ser levels have been determined in a cohort of elderly subjects encompassing the entire continuum from fitness to frailty. D-Ser and D-/total Ser ratio were independent predictors of Edmonton Frail Scale (EFS). Furthermore, higher levels of Gly, Gly/L-Ser and D-/total Ser were associated with worse cognition and depressive symptoms in the frail group. These findings suggest that changes in peripheral glycine and serine enantiomers homeostasis may represent a novel biochemical correlate of frailty.

INTERACT: a randomized phase 2 study of the DAAO inhibitor luvadaxistat in adults with schizophrenia

Murthy V, Hanson E, DeMartinis N, Asgharnejad M, Dong C, Evans R, Ge T, Dunayevich E, Singh JB, Ratti E, Galderisi S. Schizophr Res. 2024 Jun 28;270:249-257. doi: 10.1016/j.schres.2024.06.017. Online ahead of print. Luvadaxistat (TAK-831/NBI-1065844) is a D-amino acid oxidase (DAAO) inhibitor that increases D-Ser levels at NMDAR coagonist sites. INTERACT is a phase 2 randomized, placebo-controlled study (ClinicalTrials.gov: NCT03382639) that evaluated the efficacy and safety of three doses of luvadaxistat in patients with schizophrenia with persistent negative symptoms. The study included a 14-day, single-blinded placebo run-in period and a 12-week, double-blinded treatment period. No significant improvements in Positive and Negative Syndrome Scale-Negative Symptom Factor Score (PANSS NSFS) were observed at any dose versus placebo at week 12. Improvements were observed with luvadaxistat 50 mg versus placebo in cognitive endpoints: Brief Assessment of Cognition in Schizophrenia (BACS) composite score and SCoRS interviewer total score. Luvadaxistat did not significantly improve negative symptoms of schizophrenia. However, luvadaxistat 50 mg met the prespecified secondary endpoints for cognitive (BACS) and function (SCoRS), warranting further investigation in patients with cognitive impairment associated with schizophrenia. Luvadaxistat was welltolerated.

New drug treatments for schizophrenia: a review of approaches to target circuit dysfunction

Howes OD, Dawkins E, Lobo MC, Kaar SJ, Beck K. Biol Psychiatry. 2024. May 28:S0006-3223(24)01349-0. Online ahead of print doi: 10.1016/j.biopsych.2024.05.014. Schizophrenia is a leading cause of global disease burden. Current drug treatments are associated with significant side effects and have limited efficacy for many patients, highlighting the need to develop new approaches. Among the others, drugs for GABAergic or glutamatergic targets, including glycine transporters, Damino acid oxidase, sodium channels, or potassium channels, have been proposed.

D-AAS & PHYSIOLOGICAL ROLES:

D-aspartate, an amino-acid important for human health, supports anaerobic respiration in several Campylobacter species

Benoit SL, Maier RJ. Res Microbiol. 2024. Jun 28:104219. doi: 10.1016/j.resmic.2024.104219. Online ahead of print. Most Campylobacter species can grow anaerobically, using formate or molecular hydrogen (H2) as electron donors, and various nitrogenous and sulfurous compounds as electron acceptors. Herein, it has been reported that both L-Asn and L-Asp bolster H2-driven anaerobic growth in several Campylobacter species, whereas the D-enantiomers only increased anaerobic growth in Campylobacter concisus strain 13826 and Campylobacter ureolyticus strain NCTC10941. A gene annotated as racD encoding for a putative D/L-Asp racemase was identified in the genome of both strains: results suggest that the racD gene is required for campylobacters to use either D-Asp or D-Asn. This is the first report of human pathogens scavenging a D-amino acid essential for human health.

Effects of eyestalk ablation and seawater temperature on D-glutamate levels in the reproductive tissues of male kuruma prawn Marsupenaeus japonicus

Yoshikawa N, Yoshitomi N, Nakada K. J Biochem. 2024. May 22:mvae036. doi: 10.1093/jb/mvae036. Online ahead of print. D-Glu exclusively exists in the male reproductive tissues of kuruma prawn Marsupenaeus japonicus. The D-Glu content in the testis increased with increasing seawater temperature, and with unilateral eyestalk ablation. This suggests that both stimulations induced D-Glu synthesis in the testis. Although the D-Ala content in the testis increased after unilateral eyestalk ablation, it did not change with elevated seawater temperature. The work suggests that D-Glu is crucial in prawn fertilization.

D-AAS & BIOTECHNOLOGY:

A dual-function selection system enables positive selection of multigene CRISPR mutants and negative selection of Cas9-free progeny in Arabidopsis

Wang FZ, Bao Y, Li Z, Xiong X, Li JF. aBIOTECH. 2024. Jan 22;5(2):140-150. Jun. doi: 10.1007/s42994-023-00132-6. eCollection 2024 The CRISPR/Cas9 technology revolutionizes targeted gene knockout in diverse organisms including plants. However, screening edited alleles, particularly those with multiplex editing, from herbicide- or antibioticresistant transgenic plants and segregating out the Cas9 transgene represent two laborious processes. Here, a Trigonopsis variabilis D-amino acid oxidase (TvDAAO)-based selection system that simultaneously enables the enrichment of multigene edited alleles and elimination of Cas9-containing progeny in Arabidopsis thaliana was set up. Transgenic expression of TvDAAO in Arabidopsis allowed a clear distinction between transgenic and nontransgenic plants in both D-Ser-conditioned positive selection and D-Val-conditioned negative selection. This represents a novel strategy to ease CRISPR mutant identification and Cas9 transgene elimination using a single selection marker.

Biosynthesis of α-keto acids and resolution of chiral amino acids by L-amino acid deaminases from Proteus mirabilisChang J, Zhang Y, Li Z, Ma Y, Hu X, Yang J, Zhang H. Protein Expr Purif. 2024. Sep;221:106518. doi: 10.1016/j.pep.2024.106518. Epub 2024 May 29. Chiral amino acids and their deamination products, α-keto acids, have important applications in food, medicine, and fine chemicals. In this study, two L-amino acid deaminase genes from Proteus mirabilis, PM473 of type Ⅰ and PM471 of type Ⅱ were cloned and expressed in Escherichia coli: PM473 has a wider catalytic range for amino acids. When D,L-Cys was used as the substrate, all L-Cys components and 75.1 % of D-Cys were converted to mercapto pyruvate, and the remaining D-Cys was a single enantiomer.

Effect of novel and traditional intracanal medicaments on biofilm viability and composition

Siu SY, Pudipeddi A, Vishwanath V, Cheng Lee AH, Tin Cheung AW, Pan Cheung GS, Neelakantan P. J Endod. 2024. Jul 15:S0099-2399(24)00398-4. doi: 10.1016/j.joen.2024.07.003. Online ahead of print. This study evaluated the hypothesis that a combination of D-amino acids (D-AA) and trans-cinnamaldehyde (TC) has superior antibiofilm activity to calcium hydroxide (CH) and untreated controls. The concentration of D-AAs (D-Met, D-Leu, D-Tyr, and D-Trp) that would significantly decrease Enterococcus faecalis and Actinomyces naeslundii biofilm biomass was determined, and then the effect of TC + selected D-AAs on polymicrobial biofilms was characterized. TC (0.06%) + D-Tyr (1 mM) + D-Trp (25 mM) significantly reduced the biomass and biofilm viability compared to the control, also giving greater percentage of dead bacteria and decreased biovolume.

Designed de novo α-sheet peptides destabilize bacterial biofilms and increase the susceptibility of E. coli and S. aureus to antibiotics

Prosswimmer T, Nick SE, Bryers JD, Daggett V. Int J Mol Sci. 2024. Jun 27;25(13):7024. doi: 10.3390/ijms25137024. Biofilm-associated microbes are 10-1000 times less susceptible to antibiotics. An emerging treatment strategy is to target the structural components of biofilm to weaken the extracellular matrix without introducing selective pressure. This work investigated the impact of inhibiting amyloid formation on antibiotic susceptibility. Two αsheet peptides, AP90 (L-amino acid dominant) and AP401 (D-amino acid dominant), with the same sequence but inverse chirality at every amino acid were tested. For E. coli, both peptides increased antibiotic susceptibility and decreased the biofilm colony forming units when administered with five different antibiotics, and AP401 caused a greater increase in all cases. For S. aureus, increased biofilm antibiotic susceptibility was observed for both peptides, but AP90 outperformed AP401. Chirality influences biofilm targeting of Gram-negative E. coli and Gram-positive S. aureus.

A near-infrared broad-spectrum antimicrobial nanoplatform powered by bacterial metabolic activity for enhanced antimicrobial photodynamic-immune therapy

Zheng J, Meng W, Chen S, Cui Z, Xian X, Tian J, Krysko DV, Li B, Zhang W. Acta Biomater. 2024. Jun 25:S1742-7061(24)00338-6. doi: 10.1016/j.actbio.2024.06.024. Online ahead of print. This work is aimed at introducing an innovative near-infrared antimicrobial nanoplatform (ZFC) driven by bacterial metabolism. ZFC, comprising D-Cys-functionalized pentafluorophenyl bacteriochlorin (FBC-Cy) coordinated with Zn2+, is designed for antimicrobial photodynamic-immune therapy (aPIT) against systemic bacterial infections. By specifically targeting bacteria via D-amino acid incorporation into the peptidoglycan, ZFC achieves precise bacterial clearance in wound and pulmonary infections, exhibiting an antimicrobial efficacy of up to 90% with minimal damage to normal cells under 750 nm light. Additionally, ZFC enhances the activation of antigen-presenting cells by 3.2-fold compared to control groups and aPIT induced by ZFC triggers systemic immune responses and establishes immune memory.

Pilot evaluation of S-(3-[(18)F]fluoropropyl)-D-homocysteine and O-(2[(18)F]fluoroethyl)-D-tyrosine as bacteria-specific radiotracers for PET imaging of infection

Betts HM, Luckett JC, Hill PJ. Mol Imaging Biol. 2024. Jun 28. doi: 10.1007/s11307-024-01929-7. Online ahead of print. This work describes fluorine-18 labelled analogues of D-Tyr and D-Met, O-(2-[18F]fluoroethyl)-D-Tyr (D-[18F]FET) and S-(3-[18F]fluoropropyl)-D-homocysteine (D-[18F]FPHCys), and their evaluation studies as potential radiotracers for imaging bacterial infection. In vitro uptake of both D-[18F]FET and D-[18F]FPHCys was specific to live bacteria. Uptake was higher in S. aureus than in P. aeruginosa for both radiotracers. In vivo, D[18F]FPHCys had greater accumulation in S. aureus infection compared with sterile inflammation, which was statistically significant. As anticipated, [18F]FDG showed no significant difference in uptake between infection and inflammation.

Inverted amino acids reduce the adhesion and biofilm biomass of early oral colonizers

Wijesinghe GK, Nissanka M, Maia FC, Rossini de Oliveira T, Höfling JF. Dent Med Probl. 2024. May-Jun;61(3):385-390. doi: 10.17219/dmp/160092. Early colonizers adhere to the dental surface and facilitate the initial adhesion of secondary colonizers to form oral biofilms, which may cause oral infections. This study aimed to determine the antimicrobial, anti-adhesion and antibiofilm potency of (inverted) D-amino acids on early colonizer streptococci and their mixed species. No minimum inhibitory concentration (MIC) point was detected at any concentration tested. The minimum bactericidal concentration (MBC) point was not observed too. The adhesion of S. mitis, S. oralis and mixed species was reduced by all tested D-AAs. No adverse effects were observed on S. gordonii with any of the tested D-AAs. The biofilm biomass of test strains under flow conditions was significantly reduced after a 5-min exposure to all tested D-AAs at 25 mM concentration.

ENZYMES ACTIVE ON D-AAS:

Enhancing the amination activity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum by modifying the crucial residue His154 for deamination

Yuan K, Huo Z, Zhang YN, Guo Z, Chang Y, Jin Y, Gao L, Zhang T, Li Y, Ma Q, Gao X. J Biotechnol. 2024. Jul 18:S0168-1656(24)00199-8. doi: 10.1016/j.jbiotec.2024.07.015. Online ahead of print. In the deamination and amination reaction of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum (StDAPDH), H154 has been proposed as a basic residue that facilitates water molecules to attack the D-carbon of meso-DAP during deamination. Site saturation mutagenesis results showed that almost all of the H154 variants completely lost the deamination activity towards meso-DAP, and some of them showed enhanced kcat/Km values towards pyruvic acid and other bulky 2-keto acids. When combined with the previously reported W121L/H227I variant, the triple variant showed significantly improved kcat/Km values towards these 2keto acids.

Through virtual saturation mutagenesis and rational design for superior substrate conversion in engineered D-amino acid oxidase

Tang H, Zhu HL, Zhao JQ, Wang LY, Xue YP, Zheng YG. Biotechnol J. 2024. Jul;19(7):e2400287. doi: 10.1002/biot.202400287. D-amino acid oxidase from Rasamsonia emersonii (ReDAAO) can be used to produce optically pure Lglufosinate (L-PPT) by converting D-glufosinate (D-PPT) to its deamination product. Using Caver 3.0 and alanine scanning, the key residues close to three substrate binding pockets were identified. Virtual saturation mutagenesis (VSM), and experimentally validated variants which reduced substrate binding energy were studied revealing elongated side-chain prevalence in substrate binding pocket periphery. Employing VSM-assisted screening multiple times and after four rounds of combining mutations, the N53V/F57Q/V94R/V242R variant was generated, resulting in a > 5000% increase in enzyme activity compared to the wild-type.

A novel series of metazoan L/D peptide isomerases

Andersen HM, Tai HC, Rubakhin SS, Yau PM, Sweedler JV. J Biol Chem. 2024. Jun 8;300(7):107458. doi: 10.1016/j.jbc.2024.107458. Online ahead of print. Here, the characterization of putative peptide isomerase enzymes extracted from R. norvegicus, A. californica, and B. taurus tissues was reported. These enzymes are both tissue and substrate-specific across all three organisms. Notably, the lungs of the mammalian species, and the central nervous system of the mollusk displayed the highest isomerase activity among the examined tissues. In vitro enzymatic conversion was observed for several endogenous peptides. By using several inhibitors on these enzymes, common active site residues have been suggested. This study emphasizes a widespread and overlooked enzyme activity related to the creation of bioactive peptides.

Mechanism-guided computational design drives meso-diaminopimelate dehydrogenase to efficient synthesis of aromatic D-amino acids

Wu T, Chen Y, Wei W, Song W, Wu J, Wen J, Hu G, Li X, Gao C, Chen X, Liu L. ACS Synth Biol. 2024. Jun 21;13(6):1879-1892. doi: 10.1021/acssynbio.4c00176. Epub 2024 Jun 7. Aromatic D-amino acids (D-AAs) play a pivotal role as important chiral building blocks and key intermediates in fine chemical and drug synthesis. Meso-diaminopimelate dehydrogenase (DAPDH) serves as biocatalyst in the synthesis of D-AAs and their derivatives. This study elucidated the catalytic mechanism underlying DAPDH from Proteus vulgaris (PvDAPDH) through the examination of its crystallographic structure, computational simulations of potential energies and molecular dynamics simulations, and site-directed mutagenesis. The PvDAPDH-M3 variant showed an increased specific activity and catalytic efficiency (kcat/Km) for aromatic keto acids up to 124-fold and 92-fold, respectively, compared to the wild type. Additionally, it expanded the substrate scope to 10 aromatic keto acid substrates. Finally, six high-value-added aromatic D-AAs and their derivatives were synthesized using a one-pot three-enzyme cascade reaction, exhibiting a good conversion rate ranging from 32 to 84% and excellent stereoselectivity (enantiomeric excess >99%).

Development of growth selection system and pocket engineering of D-amino acid oxidase to enhance selective deamination activity toward D-phosphinothricin

Cheng F, Sun KX, Gong XX, Peng W, Zhang HY, Liang XH, Xue YP, Zheng YG. Biotechnol Bioeng. 2024. Jun 1. doi: 10.1002/bit.28763. Online ahead of print. D-amino acid oxidase (DAAO)-catalyzed selective oxidative deamination is a very promising process for synthesizing L-amino acids including L-phosphinothricin (L-PPT, a high-efficiency and broad-spectrum herbicide). Here, the DAAO from Caenorhabditis elegans (CeDAAO) was screened and engineered to improve the catalytic potential on D-PPT. The paper reports on the production of an enzyme variant enabling the efficient synthesis of L-PPT.

D-AAS IN MICROORGANISMS:

Evidence for archaeal metabolism of D-amino acids in the deep marine sediments

Yu Y, Liu NH, Teng ZJ, Chen Y, Wang P, Zhang YZ, Fu HH, Chen XL, Zhang YQ. Sci Total Environ. 2024. Jul 11;948:174723. doi: 10.1016/j.scitotenv.2024.174723. Online ahead of print. The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. D-amino acids (D-AAs) and D-AA-containing muropeptides, are primarily derived from bacterial peptidoglycan decomposition. This study reports a bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in D-AA metabolism. Our analyses suggest that a variety of archaea, particularly Candidatus bathyarchaeota and Candidatus lokiarchaeaota, can metabolize DAAs. D-AAs are converted into L-amino acids via amino acid racemases, and converted into α-keto acid via Dserine ammonia-lyase, whereas D-AA-containing di-/tri-muropeptides are hydrolyzed by peptidases (dipeptidase and D-aminopeptidase).

D-AAS IN PEPTIDES AND PROTEINS:

Brain-targeted drug delivery by in vivo functionalized liposome with stable Dpeptide ligand

Yang Y, Chu Y, Li C, Fan L, Lu H, Zhan C, Zhang Z. J Control Release. 2024. Jul 18;373:240-251. doi: 10.1016/j.jconrel.2024.07.014. Online ahead of print. Brain-targeted drug delivery poses a great challenge due to the blood-brain barrier (BBB). A previous study developed a peptide-modified stealth liposome (SP-sLip) to enhance BBB penetration via the adsorption of apolipoproteins in plasma. SP is an 11-amino acid peptide derived from 25 to 35 of the Amyloid β peptide (Aβ142), a ligand of apolipoproteins. Here, a D-peptide ligand according to the reverse sequence of SP with Damino acids, known as DSP, was designed: it exhibited lower self-aggregation and improved stability, prolonged blood circulation, reduced liver and spleen accumulation with comparable brain-targeting efficiency. Similar to SP-sLip, DSP-sLip selectively adsorbed apolipoprotein A1, E, and J in the blood to form functionalized protein corona, thus crossing BBB via apolipoprotein receptor-mediated transcytosis.

How D-amino acids embedded in the protein sequence modify its digestibility: Behaviour of digestive enzymes tested on a model peptide used as target

Accardo F, Prandi B, Dellafiora L, Tedeschi T, Sforza S. Food Chem. 2024. Jun 25;458:140175. doi: 10.1016/j.foodchem.2024.140175. Online ahead of print. D-amino acids (D-AAs) can affect the action of digestive enzymes, hence the protein digestion. In this work the behaviour of the main stomach and gut digestive enzymes (pepsin, trypsin, and chymotrypsin) in the presence of D-AAs in the protein chain was monitored over time using a model peptide, Ac-LDAQSAPLRVYVE-NH2 (belonging to β-lactoglobulin), where L-amino acids were systematically substituted by D-AAs. Various alterations were apparent in the behaviour of digestive enzymes, not only when the D-AAs are inserted at the specific cleavage sites (after Val-57), but in some cases also when in distant positions. The effect seemed more pronounced in the case of pepsin rather than the gut enzymes.

Peptidomimetic inhibitors targeting TrkB/PSD-95 signaling improves cognition and seizure outcomes in an Angelman Syndrome mouse model

Huie EZ, Yang X, Rioult-Pedotti MS, Naik M, Huang YA, Silverman JL, Marshall J. bioRxiv [Preprint]. 2024. Jun 8:2024.06.07.597833. doi: 10.1101/2024.06.07.597833. Angelman syndrome (AS) is a rare genetic neurodevelopmental disorder with profoundly debilitating symptoms with no FDA-approved cure or therapeutic. It has been suggested that drugs tailored to enhance the TrkB-PSD95 interaction may provide a novel approach for the treatment of AS and a variety of NDDs. To evaluate this critical interaction, a class of high-affinity PSD-95 ligands that bind specifically to the PDZ3 domain, were generated. In this work Syn3 and its analog D-Syn3 (engineered using D-amino acids) was tested in vivo using the Ube3a exon 2 deletion mouse model of AS, demonstrating improvement in the seizure domain of AS. Learning and memory using the novel object recognition assay also illustrated improved cognition following Syn3 and D-Syn3, along with restored long-term potentiation. Finally, D-Syn3 treated mice showed a partial rescue in motor learning.

Optimization of the antifungal properties of the bacterial peptide EntV by variant analysis

Guha S, Cristy SA, Buda De Cesare G, Cruz MR, Lorenz MC, Garsin DA. mBio. 2024. May 8;15(5):e0057024. doi: 10.1128/mbio.00570-24. Epub 2024 Apr 9. Fungal resistance to commonly used medicines is a growing public health threat, and there is a dire need to develop new classes of antifungals. These authors previously described a peptide produced by Enterococcus faecalis, EntV, that restricts Candida albicans to a benign form rather than having direct fungicidal activity. Chemical modifications to the peptides to increase stability, including substitutions of D-amino acids and hydrocarbon stapling, were investigated. The most promising peptides were additionally tested in mouse models of oropharyngeal and systemic candidiasis where their efficacy in preventing infection was demonstrated.

Design of proteolytic-resistant antifungal peptides by utilizing minimum D-amino acid ratios

Lai Z, Yuan X, Chen W, Chen H, Li B, Bi Z, Lyu Y, Shan A. J Med Chem. 2024. Jul 11;67(13):10891-10905. doi: 10.1021/acs.jmedchem.4c00394. Epub 2024 Jun 27. In this work a library was set up to design peptides with protease resistance and high antifungal activity. The peptides were incorporated with minimal D-amino acids to further improve the protease stability. The most active peptide, IR3, demonstrated good antifungal activity. low toxicity, and resistance to protease hydrolysis. Furthermore, IR3 could permeate the fungal cell wall, disrupt the cell membrane, produce reactive oxygen species, and induce apoptosis in fungal cells. In vivo experiments confirmed that IR3 could effectively treat fungal keratitis.

D-AAS IN PEPTIDES AND PROTEINS:

Electrochemical chiral sensor developed using nanofibrous polyaniline chiral structures: detection and differentiation of D- and L-tryptophan

Viji P., Ganesh V. Journal of Electroanalytical Chemistry. 2024. 968, art. no. 118494. DOI: 10.1016/j.jelechem.2024.118494 This work reports on a simple strategy for electrochemical detection and differentiation of D- and L-enantiomers of tryptophan is demonstrated using nanofibrous structures of chiral polyaniline (CP). Basically, CP with desired chirality is prepared using a chiral acid, namely ± camphor sulfonic acid (±CSA) in presence of either a cationic (or) anionic surfactant (CTAB / SDS) through a simple oxidative polymerization process. This CP materials are found to be electrochemically selective for the detection and differentiation of D- and L-Trp. (LOD of 0.98 µM for L-Trp and 1.2 µM for D-Trp).

Characterisation of a microelectrochemical biosensor for real-time detection of brain extracellular D-serine

Doran MM, Bermingham KP, Tricklebank MD, Lowry JP. Talanta. 2024. Jun 22;278:126458. doi: 10.1016/j.talanta.2024.126458. Online ahead of print. In this paper, a modified protocol and the characterisation of a first generation biosensor for the detection of brain extracellular D-Ser is reported, a sensor based on D-amino acid oxidase (DAAO) and a dip-coating immobilisation method employing a new extended drying approach. The resultant Pt-based polymer enzyme composite sensor achieved high sensitivity to D-Ser (0.76 nA/mm2 μM) and a low LOD (0.33 μM). The in vitro response time was within the solution stirring time, suggesting potential sub-second in-vivo response. Potential interference signals generated by the principal electroactive analytes present in the brain were minimised by using a permselective layer of poly(o-phenylenediamine). The biosensor was implanted in the striatum of freely moving rats and used to monitor physiological changes in D-Ser over a two-week period.

An enantioselective fluorescent probe for detecting arginine and glutamic acids

Zhang B, Zhou F, Yu X, Zhang P, Sun X, Su J, Fan C, Shu W, Dong Q, Zeng C. Food Chem. 2024. Oct 15;455:139976. doi: 10.1016/j.foodchem.2024.139976. Epub 2024 Jun 4. These authors synthesized fluorescent probe (R)-5 by condensation of 1,1′-bi-2-naphthol (BINOL) and 2(aminomethyl)pyridine with Schiff base, which can recognize both D-Arg and D-Glu at low concentrations. Meanwhile, (R)-5 can be applied to paper-based sensors for the detection of arginine and glutamate in living cells and for food amino acid detection.

HPLC with chiral stationary phase for separation and kinetics study of aspartic acid epimerization in Peroxiredoxin 2 active site peptide

Zhang X, Abdulbagi M, Wang L, Wang J, Di B, Li B. J Pharm Biomed Anal. 2024. Sep 1;247:116247. doi: 10.1016/j.jpba.2024.116247. Epub 2024 May 21. Amino acid epimerization, a process of converting L-amino acids to D-amino acids, will lead to modification in the protein structure and, subsequently, its biological function. Aspartic Acid Epimerization (AAE) is faster than other amino acids and could be accelerated by free radicals and peroxides. In this work, a novel and sitespecific HPLC method using a chiral stationary phase for determining the AAE in the active site model peptide (AP) of Peroxiredoxin 2 has been developed and validated. This method showed good linearity (1 – 200 μg/mL) and recoveries of the limit of quantification (LOQ), low, medium, and high concentrations were between 85% and 115%. The kinetics of AAE in AP were studied using the developed method, showing that when ascorbic acid and Cu2+ coexisted, the AP epimerized rapidly.

INFORMATION

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).

Info@d-aminoacids.com

director@d-aminoacids.com

D-AMINO ACIDS INTERNATIONAL RESEARCH CENTER

INFO@D-AMINOACIDS.COM