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The Editor’s pick selection of the most intriguing papers is highlighted in yellow.
D-AAs AND PATHOLOGIES:
- D-aspartate oxidase gene duplication induces social recognition memory deficit in mice and intellectual disabilities in humans
Lombardo, B., Pagani, M., De Rosa, A., Nunziato, M., Migliarini, S., Garofalo, M., Terrile, M., D’Argenio, V., Galbusera, A., Nuzzo, T., Ranieri, A., Vitale, A., Leggiero, E., Di Maio, A., Barsotti, N., Borello, U., Napolitano, F., Mandarino, A., Carotenuto, M., Heresco-Levy, U., Pasqualetti, M., Malatesta, P., Gozzi, A., Errico, F., Salvatore, F., Pastore, L., Usiello, A.
Translational Psychiatry, 2022, 12 (1), art. no. 305, . DOI: 10.1038/s41398-022-02088-5
To clarify the role of D-aspartate on brain development and functioning, here a mouse model with constitutive Ddo overexpression (the gene encoding D-aspartate oxidase, DDO or DASPO) and D-aspartate depletion was used. In these mice, a reduced number of BrdU-positive dorsal pallium neurons during corticogenesis, and a decreased cortical and striatal gray matter volume at adulthood was found. These mice showed social recognition memory deficit at juvenile phase, suggesting that early D-aspartate occurrence influences neurodevelopmental related phenotypes. Furthermore, the first clinical case of a young patient with severe intellectual disability, thought disorders and autism spectrum disorder symptomatology, harboring a duplication of a chromosome 6 region, including the entire Ddo gene, was also reported.
- D-Alanine as a biomarker and a therapeutic option for severe influenza virus infection and COVID-19
Kimura-Ohba, S., Asaka, M.N., Utsumi, D., Takabatake, Y., Takahashi, A., Yasutomi, Y., Isaka, Y., Kimura, T.
(2023) Biochimica et Biophysica Acta – Molecular Basis of Disease, 1869 (1), art. no. 166584 DOI: 10.1016/j.bbadis.2022.166584
This interesting work reports that in mice infected with influenza A virus (IAV) and in patients with severe COVID-19 (requiring artificial ventilation or extracorporeal membrane oxygenation), blood levels of D-amino acids were significantly decreased compared with healthy controls. In both pathological conditions, D-alanine supplementation alleviated severity of clinical course. Furthermore, mice with sustained blood levels of D-alanine showed favorable prognoses. Accordingly, D-alanine has great potentials as a biomarker and a therapeutic option for severe viral infections.
- Precolumn derivatization LC/MS method for observation of efficient hydrogen sulfide supply to the kidney via D-cysteine degradation pathway
Sugiyama, E., Higashi, T., Nakamura, M., Mizuno, H., Toyo’oka, T., Todoroki, K.
(2023) Journal of Pharmaceutical and Biomedical Analysis, 222, art. no. 115088, DOI: 10.1016/j.jpba.2022.115088
In this paper, the levels of D-cysteine (D-Cys) and hydrogen sulfide (H2S), were determined using a new method with no detectable isomerization of Cys and an established method for H2S, respectively. The derivatives were determined by LC/MS using a C18 column. The results show that D-amino acid oxidase inhibition significantly suppressed the H2S supplementation and the D-Cys degradation in the mouse kidney, and that D-Cys is more efficiently metabolized into H2S than L-Cys. This is of main relevance since D-Cys is metabolized to H2S by D-amino acid oxidase/3-mercaptopyruvate sulfurtransferase pathway, which is required for H2S supplementation that ameliorates acute kidney injury after the oral administration of D-Cys in mice.
- Pharmacokinetics and safety of sodium benzoate, a D-amino acid oxidase (DAAO) Inhibitor, in healthy subjects: a phase I, open-label study
Yen-Shan Lin, Wei-Chung Mao, Nai-Tzu Yao, Guochuan Emil Tsai
Clin Ther. 2022 Oct;44(10):1326-1335. doi: 10.1016/j.clinthera.2022.08.008
Sodium benzoate is a D-amino acid oxidase (DAAO) inhibitor that allows the increase of D-serine levels and that enhances N-methyl-D-aspartate receptor functions as a therapeutic agent for various central nervous system disorders, e.g. schizophrenia and dementia. Here, a phase I study was carried out to evaluate benzoate safety, tolerability, and pharmacokinetic profile after single-dose oral administration in healthy volunteers exposed to 250, 500, 1000, and 2000 mg of sodium benzoate. Interestingly, sodium benzoate treatment exhibited a favorable safety profile and was well tolerated at all dose levels.
- Endogenous antioxidants predicted outcome and increased after treatment: a benzoate dose-finding, randomized, double-blind, placebo-controlled trial for Alzheimer’s disease
Hsien-Yuan Lane,Shi-Heng Wang,Chieh-Hsin Lin
Psychiatry and Clinical neurosciences, First published: 06 November 2022, https://doi.org/10.1111/pcn.13504
Benzoate, a well-known D-amino acid oxidase inhibitor, has been suggested as a potential cognitive enhancer for patients with Alzheimer’s disease (AD), schizophrenia, or late-life depression. Here, a 24-week, dose-finding, randomized, double-blind, placebo-controlled trial, with clinical measurements at weeks 0, 8, 16, and 24, was conducted in three major medical centers in Taiwan. The benzoate 1000 group (500 mg/day for the first 4 weeks, 1000 mg/day from the 5th week) performed better in improving the AD assessment scale-cognitive subscale ADAS-cog, with female advantage. By enhancing two vital endogenous antioxidants, catalase and glutathione, sodium benzoate therapy improved cognition of patients with AD.
- The D-serine biosynthetic enzyme serine racemase is expressed by reactive astrocytes in the amygdala of human and a mouse model of Alzheimer’s disease
Oluwarotimi O Folorunso, Theresa L Harvey, Stephanie E Brown, Gabriele Chelini, Sabina Berretta, Darrick T Balu
Neurosci Lett. 2022 Nov 7;792:136958. doi: 10.1016/j.neulet.2022.136958.
This work reports that C3 + reactive astrocytes express serine racemase (SR, the enzyme deputed to produce the N-methyl-D-aspartate receptor (NMDAR) co-agonist D-serine) in the amygdala of Alzheimer’s disease (AD) patients and in an amyloid mouse model of familial AD (5xFAD). The authors suggest that D-serine produced by reactive astrocytes in the amygdala could contribute to glutamate excitotoxicity and neurodegeneration observed with AD progression.
- D-DOPA is a potent, orally bioavailable, allosteric inhibitor of glutamate carboxypeptidase II
Sadakatali S Gori, Ajit G Thomas, Arindom Pal, Robyn Wiseman, Dana V Ferraris, Run-Duo Gao, Ying Wu, Jesse Alt, Takashi Tsukamoto, Barbara S Slusher, Rana Rais
Pharmaceutics, 2022 Sep 23;14(10):2018. doi: 10.3390/pharmaceutics14102018.
Glutamate carboxypeptidase-II is a Zn-dependent metalloenzyme implicated in numerous neurological disorders. Here, catechol-based inhibitors including L-DOPA, D-DOPA, and caffeic acid, with sub-micromolar potencies, were described. D-DOPA was the most promising compound (acting as a noncompetitive, allosteric inhibitor), with good metabolic stability, and excellent PK properties, although its brain exposures were low. The plasma and brain exposures were significantly increased when D-DOPA was used in combination with the D-amino acid oxidase (DAAO) inhibitor sodium benzoate (the inversion of D-DOPA into L-DOPA via DAAO was previously reported in literature).
- Promising application of D-amino acids toward clinical therapy
Yoahpoing Shi, Zahid Hussain, Yufen Zhao
Int J Mol Sci. 2022 Sep 16;23(18):10794. doi: 10.3390/ijms231810794.
In recent years, increasing evidence has revealed that D-amino acids have great potential in treating various diseases. E.g., D-amino acids showed overwhelming success in disengaging biofilm, in limiting the growth of cancer cells, in ameliorating reproduction function, and for treating neurological disease or tissue/organ injury. This review summarizes some relevant results in the field.
- Targeting D-amino acid oxidase (DAAO) for the treatment of schizophrenia: rationale and current status of research
Chien-Yi Kuo, Chieh-Hsin Lin, Hsien-Yuan Lane
CNS Drugs, 2022 Nov;36(11):1143-1153. doi: 10.1007/s40263-022-00959-5.
This review reports on current research in D-amino acid oxidase (DAAO) inhibitors. In the brain, DAAO deaminates D-serine, the main coagonist of N-methyl-D-aspartate receptors (NMDARs). NMDAR hypofunction is related to the pathogenesis of schizophrenia. On this side, patients with schizophrenia show lower D-serine levels in peripheral blood and cerebrospinal fluid and higher DAAO expression and activity in the brain. Slowing D-serine degradation by using DAAO inhibitors represents a way to enhance NMDAR function, strategy to treat schizophrenia.
D-AAs AND BACTERIA:
- Fluorescent D-amino acids for super-resolution microscopy of the bacterial cell wall
Chen Zhang, Luc Reymond, Ophélie Rutschmann, Mischa A. Meyer, Julien Denereaz, Jiangtao Qiao, Faustine Ryckebusch, Juliette Griffié, Willi L. Stepp, Suliana Manley
ACS Chem. Biol. 2022, 17, 9, 2418–2424 https://doi.org/10.1021/acschembio.2c00496
This work focuses on the synthesis and characterization of new fluorescent D-amino acids (FDAAs) compatible with one-step labeling and single molecule localization microscopy (SMLM) imaging. The incorporation of the selected probes and their utility for visualizing peptidoglycan at the nanoscale was demonstrated in Gram-negative, Gram-positive, and mycobacteria species.
D-AAs AND BIOTECHNOLOGY:
- Direct fluorescence evaluation of D-amino acid oxidase activity using a synthetic D-kynurenine derivative
Sakamoto, T., Odera, K., Onozato, M., Sugasawa, H., Takahashi, R., Fujimaki, Y., Fukushima, T.
(2022) Analytical Chemistry, 94 (42), pp. 14530-14536. DOI: 10.1021/acs.analchem.2c00775
Here, the nonfluorescent 5-methylthio-D-kynurenine (MeS-D-KYN) was synthesized. This compound can be converted by D-amino acid oxidase (DAAO) to blue-fluorescent 6-MeS-kynurenic acid (MeS-KYNA). The fluorescence intensity increased when incubated with a commercial DAAO preparation. MeS-D-KYN was applied to fluorescent DAAO imaging in cultured LLC-PK1 cells: the blue fluorescence of MeS-KYNA overlapped considerably with the signal for peroxisomes. MeS-D-KYN seems a suitable compound to assay DAAO activity.
- Hydrophilicity-based engineering of the active pocket of D-amino acid oxidase leading to highly improved specificity toward D-glufosinate
Kai Yang, Bin Huang, Charles Amanze, Zhen Yan, Guanzhou Qiu, Xueduan Liu, Hongbo Zhou, Weimin Zeng
Volume 61, Issue 46 November 14, 2022 e202212720 https://doi.org/10.1002/anie.202212720
Hydrophilicity-based triple-code site-directed mutagenesis (S-T-Q) was applied to the wild-type D-amino acid oxidase from Rhodotorula gracilis (RgDAAO), leading to the Zn7 variant with >2000-fold improvement in specific activity toward the unnatural substrate D-glufosinate, which was thus converted into PPO, a precursor of the herbicide L-PPT. Computational analysis revealed that the higher activity was mainly due to an extended reaction pocket with greater hydrophilicity. This investigation established an enzymatic route to L-PPT production, an excellent herbicide.
ENZYMES ACTIVE ON D-AAs:
- The Y430F mutant of Salmonella D-ornithine/D-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site
Robert S Phillips, Kim-Ngoc Nguyen Hoang
Arch Biochem Biophys 2022 Nov 30;731:109429. doi: 10.1016/j.abb.2022.109429
Since tyrosine-430 of D-ornithine/D-lysine decarboxylase (DOKDC) was proposed to be responsible for the D-stereospecificity of the enzyme, the Y430F variant of Salmonella enterica serovar typhimurium was prepared. This variant shows decarboxylase activity with both D- and L-lysine and ornithine, which wild-type counterpart does not: these amino acids bind to form external aldimine complexes with the pyridoxal-5′-phosphate. The crystal structures of Y430F bound to HEPES, putrescine, D-ornithine, D-lysine, and D-arginine was solved: the D-amino acids bind in the crystals forming equilibrium mixtures of gem-diamine and external aldimine complexes. Indeed, an unexpected allosteric product activator site for putrescine was identified on the 2-fold axis between the two active sites: adding putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics
- YgeA is involved in L- and D-homoserine metabolism in Escherichia coli
Tetsuya Miyamoto, Yasuaki Saitoh, Masumi Katane, Masae Sekine, Hiroshi Homma
FEMS Microbiol Lett. . 2022 Nov 17;369(1):fnac096. doi: 10.1093/femsle/fnac096.
Here, the amino acid racemase YgeA from Escherichia coli was investigated in vivo. When wild-type and ygeA-deficient E. coli strains were cultured in minimal medium containing D-homoserine, its level significantly increased in the latter strain. D-homoserine was detected in YgeA-expressed E. coli cells cultured in minimal medium containing the L-enantiomer. The growth of the ygeA-deficient strain was significantly impaired in minimal medium with or without D-homoserine supplementation, while L-methionine, L-threonine or L-isoleucine (that are produced via L-homoserine) restored the growth impairment. The wild-type strain formed biofilms significantly more efficiently than the ygeA-deficient strain, and L- or D-homoserine suppressed biofilm formation by the wild-type strain, with no effect on the ygeA-deficient strain. These results suggest that YgeA acts as an amino acid racemase and plays a role in L- and D-homoserine metabolism in E. coli.
- Characterization of human cystathionine γ-lyase enzyme activities toward D-amino acids
Tetsuya Miyamoto, Yasuaki Saitoh, Masumi Katane, Masae Sekine, Kumiko Sakai-Kato, Hiroshi Homma
Biosci Biotechnol Biochem 2022 Oct 20;86(11):1536-1542. doi: 10.1093/bbb/zbac151
Concerning the biosynthetic pathway of D-serine, in Escherichia coli the enzyme cystathionine β-lyase was reported to possess amino acid racemase activity in addition to β-lyase activity. Here, the enzymatic activities of human cystathionine γ-lyase were investigated: the enzyme did not show racemase activity toward various amino acids and lyase and dehydratase activities were highest toward L-cystathionine and L-homoserine, respectively. The enzyme showed low activity toward L-cysteine and L-serine, and no activity toward D-amino acids. Catalytic efficiency was higher for lyase activity than for dehydratase activity
D-AAs IN PEPTIDES:
- Discovery of κ opioid receptor (KOR)-selective D-tetrapeptides with improved in vivo antinociceptive effect after peripheral administration
Azzurra Stefanucci, Alice Della Valle, Giuseppe Scioli, Lorenza Marinaccio, Stefano Pieretti, Paola Minosi, Edina Szucs, Sandor Benyhe, Domiziana Masci, Parthasaradhireddy Tanguturi, Kerry Chou, Deborah Barlow, Karen Houseknecht, John M. Streicher, Adriano Mollica
ACS Med. Chem. Lett. 2022, 13, 11, 1707–1714 https://doi.org/10.1021/acsmedchemlett.2c00237
Peripherally active tetrapeptides as selective κ opioid receptor (KOR) agonists, prepared in good yields and high purity following solid-phase peptide synthesis via Fmoc protection strategy, were structurally modified at the first and second position of the lead compound FF(D-Nle)R-NH2. Aromatic side chains containing D-amino acids, such as (D)-pF-Phe, (D)-mF-Phe, (D)-oF-Phe, were introduced and led to highly selective and efficacious KOR agonists endowed with strong antinociceptive activity in vivo. The results suggest potential clinical applications in the treatment of neuropathic and inflammatory pain.
- Antibiofilm activity of LL-37 peptide and D-amino acids associated with antibiotics used in regenerative endodontics on an ex vivo multispecies biofilm model
Ana C. C. Pereira, Alana P. S. Aguiar, Leticia M. P. Araujo, Larissa O. Dantas, Marcia P. A. Mayer, Lamprini Karygianni, Thomas Thurnheer, Ericka T. Pinheiro
Life 2022, 12(11), 1686; https://doi.org/10.3390/life12111686
This study evaluated the antimicrobial effect of antibiofilm agents associated with antibiotics used in regenerative endodontic procedures (the triple antibiotic paste, TAP: ciprofloxacin + metronidazole + minocycline). An endodontic-like biofilm model grown on bovine dentin discs was used. After 21-day growth, the biofilms were treated with 1 mg/mL TAP, 10 μM LL-37, LL-37 + TAP, 40 mM D-amino acids, D-amino acids + TAP, and phosphate-buffered saline (as negative control). No significant reduction in bacterial cells was observed with TAP, LL-37, D-AAs, and D-AAs + TAP compared to the negative control, indicating a mild antibacterial activity and no activity against complex biofilms by the combination of antibiotics and D-amino acids.
- Switching the N-capping region from all-L to all-D-amino acids in a VEGF mimetic helical peptide
Lucia De Rosa, Donatella Diana, Domenica Capasso, Rachele Stefania, Rossella Di Stasi, Roberto Fattorusso, Luca Domenico D’Andrea
Molecules, 2022 Oct 17;27(20):6982. doi: 10.3390/molecules27206982
In the VEGF mimetic helical peptide QK, the N-capping region was previously demonstrated to be critical in QK helical folding. Here, the effect of the chiral inversion of the N-capping sequence on QK folding was studied by conformational analysis in solution (circular dichroism and NMR spectroscopy) as well as the effects on QK stability in serum and on proliferation
- HIV-1 gp120-CXCR4 recognition probed with synthetic nanomolar affinity D-peptides containing fragments of gp120 V3 loop
Ruohan Zhu, Qian Meng, Huijun Zhang, Ge Zhang, Lina S.M. Huang, Yan Xu, Robert T. Schooley, Jing An, Ziwei Huang
European Journal of Medicinal Chemistry Volume 244, 15 December 2022, 114797 https://doi.org/10.1016/j.ejmech.2022.114797
The HIV-1 virus recognizes the CXC chemokine receptor 4 (CXCR4) on the host cell through the third variable loop (V3 loop) of HIV-1 envelope glycoprotein gp120 during the viral entry process. The stereochemical mechanism of the molecular recognition of gp120 V3 loop with CXCR4 was studied using peptide probes containing important fragments of the V3 loop. In details, the tip and base/stem fragments of the V3 loop were linked individually with the fragment derived from another CXCR4’s chemokine ligand to generate nanomolar affinity peptide probes of the interactions. When residues of the V3 loop fragments were changed from L- to D-enantiomers, the peptides retained or had even enhanced recognition by CXCR4. The structural mechanisms of CXCR4 interactions with these peptides were investigated by site-directed mutagenesis and molecular modeling, this shedding light on the mechanisms of viral entry and of immune detection evasion
- Heterochiral dipeptide D-phenylalanyl-L-phenylalanine (H-DPhe-LPhe-OH) as a potential inducer of metastatic suppressor NM23H1 in p53 wild-type and mutant cells
Faheem, M.M., Rahim, J.U., Ahmad, S.M., Mir, K.B., Kaur, G., Bhagat, M., Rai, R., Goswami, A.
Molecular Carcinogenesis, (2022) 61 (12), pp. 1143-1160. DOI: 10.1002/mc.23465
This work identifies the heterochiral dipeptide H-DPhe-LPhe-OH (F1) as a potent inducer of the metastatic suppressor NM23H1. F1 treatment elevated p53 levels, an effect not observed in the NM23H1 knockdown condition, thus the upregulation in p53 expression by F1 is NM23H1 dependent. The antimetastatic potential of F1 is mainly mediated through NM23H1 irrespective of the p53 status of the cell. Coimmunoprecipitation studies unraveled the increase of the p53 and NM23H1 interaction in p53 wild-type cells but not in p53 mutated cells. The in vivo efficacy of F1 was then evaluated on selected mouse isogenic cell lines (4T-1 and 4T-1 p53): decreased tumor volume in the cohort injected with 4T-1 p53 cells demonstrated that while the antimetastatic potential of F1 was dependent on NM23H1, p53 activation was required for ablation of primary tumor burden. This study shows that F1 treatment induces significant abrogation of the migration, invasion and metastatic potential of both p53 wild-type and p53 deficient cancers mediated through NM23H1
- The RGD-modified self-assembling D-form peptide hydrogel enhances the therapeutic effects of mesenchymal stem cells (MSC) for hindlimb ischemia by promoting angiogenesis
Jia, P., Zhao, X., Liu, Y., Liu, M., Zhang, Q., Chen, S., Huang, H., Jia, Y., Chang, Y., Han, Z., Han, Z.-C., Li, Q., Guo, Z., Li, Z.
Chemical Engineering Journal, (2022) 450, art. no. 138004 DOI: 10.1016/j.cej.2022.138004
Mesenchymal stem cell (MSC)-based therapy represents a well-suited strategy for therapeutic angiogenesis in ischemic tissues, that can be further improved by building a supportable 3D microenvironment niche for transplanted cells. In this work, the RGD (Arg-Gly-Asp)-modified self-assembling D-form peptide hydrogel (Nap-DFDFKGRGD) was used as the co-transplantation platform for human placental MSCs (hP-MSCs). This hydrogel possessed excellent biocompatibility and biostability, exerting an anti-apoptosis capacity, improved cell viability in vitro and cell survival, and up-regulated proangiogenic cytokines of hP-MSCs in vivo. This seems a promising strategy for ischemia disease
D-AAs AND ANALYTICAL METHODS:
- Rapid, enantioselective and colorimetric detection of D-arginine
Xianzhe Yu, Binjie Zhang, Cailing Fan, Qianqian Yan, Shenglin Wang, Hui Hu, Qinxi Dong, Gengyu Du, Yanan Gao, Chaoyuan Zeng
iScience, Volume 25, Issue 9, 16 September 2022, 104964
This study focused on a strategy to incorporate multiple reaction sites on a chiral 1,1′-bi-2,2′-naphthol-based fluorescent probe, with the final aim to respond specifically to D-arginine, while producing no response with all other amino acids. The probe can be used to evaluate arginine’s concentration and enantiomeric configuration.