期刊名称:Amino Acids
期刊ISSN:0939-4451
期刊官方网站:http://www.springer.com/journal/726
出版商:Springer-Verlag Wien
出版周期:Bimonthly
影响因子:3.789
始发年份:1991
年文章数:145
是否OA:否
The first evidence of biological activity for free Hypusine, an enigmatic amino acid discovered in the '70s
Amino Acids ( IF 3.789 ) Pub Date : 2023-05-31 , DOI: 10.1007/s00726-023-03283-4
LeticiaTamborlin,KarinaDaniellePereira,DimitriusSantiagoPassosSimõesFróesGuimarães,LeonardoReisSilveira,AugustoDucatiLuchessi
Hypusine amino acid [Nε-(4-amino-2-hydroxybutyl)-lysine] was first isolated in 1971 from bovine brain extracts. Hypusine originates from a post-translational modification at the eukaryotic translation initiation factor 5A (eIF5A), a protein produced by archaebacteria and eukaryotes. The eIF5A protein is the only one described containing the hypusine residue, which is essential for its activity. Hypusine as a free amino acid is a consequence of proteolytic degradation of eIF5A. Herein, we showed, for the first time, evidence of biological activity for the free hypusine. C6 rat glioma cells were treated with hypusine, and different cellular parameters were evaluated. Hypusine treatment significantly reduced C6 cell proliferation and potently suppressed their clonogenic capacity without leading to apoptosis. Hypusine also decreased the Eif5A transcript content and the global protein synthesis profile that may occur due to negative feedback in response to high hypusine concentration, controlling the content of newly synthesized eIF5A, which can affect the translation process. Besides, hypusine treatment also altered cellular metabolism by changing the pathways for energy production, reducing cellular respiration coupled with oxidative phosphorylation, and increasing the anaerobic metabolism. These observed results and the relationship between eIF5A and tumor processes led us to test the combination of hypusine with the chemotherapeutic drug temozolomide. Combining temozolomide with hypusine reduced the MTT conversion to the same levels as those observed using double temozolomide dosage alone, demonstrating a synergetic action between the compounds. Thus, since 1971, this is the first study showing evidence of biological activity for hypusine not associated with being an essential component of the eiF5A protein. Finding out the molecular targets of hypusine are the following efforts to completely characterize its biological activity.
P19-derived neuronal cells express H1, H2, and H3 histamine receptors: a biopharmaceutical approach to evaluate antihistamine agents
Amino Acids ( IF 3.789 ) Pub Date : 2023-05-12 , DOI: 10.1007/s00726-023-03273-6
MarielaGomezPerez,GeorgianaTanasie,ArmelleTchoumiNeree,NarjaraGonzalezSuarez,ClaraLafortune,JoannePaquin,LuciaMarcocci,PaolaPietrangeli,BorhaneAnnabi,MirceaAlexandruMateescu
Histamine is a biogenic amine implicated in various biological and pathological processes. Convenient cellular models are needed to screen and develop new antihistamine agents. This report aimed to characterize the response of neurons differentiated from mouse P19 embryonal carcinoma cells to histamine treatment, and to investigate the modulation of this response by antihistamine drugs, vegetal diamine oxidase, and catalase. The exposure of P19 neurons to histamine reduced cell viability to 65% maximally. This effect involves specific histamine receptors, since it was prevented by treatment with desloratadine and cimetidine, respectively, H1 and H2 antagonists, but not by the H3 antagonist ciproxifan. RT-PCR analysis showed that P19 neurons express H1 and H2 receptors, and the H3 receptor, although it seemed not involved in the histamine effect on these cells. The H4 receptor was not expressed. H1 and H2 antagonists as well as vegetal diamine oxidase diminished the intracellular Ca2+ mobilization triggered by histamine. The treatment with vegetal diamine oxidase or catalase protected against mortality and a significant reduction of H2O2 level, generated from the cells under the histamine action, was found upon treatments with desloratadine, cimetidine, vegetal diamine oxidase, or catalase. Overall, the results indicate the expression of functional histamine receptors and open the possibility of using P19 neurons as model system to study the roles of histamine and related drugs in neuronal pathogenesis. This model is less expensive to operate and can be easily implemented by current laboratories of analysis and by Contract Research Organizations.
Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-17 , DOI: 10.1007/s00726-023-03286-1
AnthonyFeral,AnthonyRMartin,AlexandreDesfoux,MurielAmblard,LubomirLVezenkov
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens’ maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
Rationally designed PMAP-23 derivatives with enhanced bactericidal and anticancer activity based on the molecular mechanism of peptide–membrane interactions
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-13 , DOI: 10.1007/s00726-023-03290-5
HyunheeLee,Sung-HeuiShin,SungtaeYang
Antimicrobial peptides (AMPs) are a crucial component of the natural defense system that the host employs to protect itself against invading pathogens. PMAP-23, a cathelicidin-derived AMP, has potent and broad-spectrum antimicrobial activity. Our earlier studies led us to hypothesize that PMAP-23 adopts a dynamic helix–hinge–helix structure, initially attaching to membrane surfaces through the N-helix and subsequently inserting the C-helix into the lipid bilayer. Here, we rationally designed PMAP-NC with increased amphipathicity and hydrophobicity in the N- and C-helix, respectively, based on the hypothesis of the interaction of PMAP-23 with membranes. Compared to the parental PMAP-23, PMAP-NC showed two–eightfold improved bactericidal activity against both Gram-positive and Gram-negative strains with fast killing kinetics. Fluorescence studies demonstrated that PMAP-NC largely disrupted membrane integrity, indicating that efficiency and kinetics of bacterial killing are associated with the membrane permeabilization. Interestingly, PMAP-NC exhibited much better anticancer activity against tumor cells than PMAP-23 but displayed low hemolytic activity against human erythrocytes. Collectively, our findings suggest that PMAP-NC, with the structural arrangement of an amphipathic helix–hinge–hydrophobic helix that plays a critical role in rapid and efficient membrane permeabilization, can be an attractive candidate for novel antimicrobial and/or anticancer drugs.
Allyl isothiocyanate inhibits invasion and angiogenesis in breast cancer via EGFR-mediated JAK-1/STAT-3 signaling pathway
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-13 , DOI: 10.1007/s00726-023-03285-2
ThangarasuRajakumar,PachaiappanPugalendhi
Angiogenesis, invasion, and metastasis are the main events of cancer cells. JAK-1/STAT-3 is a key intracellular signaling transduction pathway, which controls the growth, differentiation, apoptosis, invasion, and angiogenesis of various cancer cells. The present study explored the impact of allyl isothiocyanate (AITC) on the JAK-1/STAT-3 pathway in DMBA-induced rat mammary tumorigenesis. The mammary tumor was initiated through a single dose of 25 mg DMBA/rat by a subcutaneous injection administered near the mammary gland. We observed decreased body weight and increased the total number of tumors, tumor incidence, tumor volume, well-developed tumor, and histopathological abnormalities in DMBA-induced rats that were modulated after being treated with AITC. Staining of mammary tissues showed a high accumulation of collagen in DMBA-induced rats and it was normalized by the AITC treatment. Moreover, DMBA-induced mammary tissues showed up-regulated expressions of EGFR, pJAK-1, pSTAT-3, nuclear fraction of STAT-3, VEGF, VEGFR2, HIF-1α, MMP-2, and MMP-9 and the down-regulated expressions of cytosolic fraction of STAT-3 and TIMP-2. Oral administration of AITC on DMBA-induced rats inhibits angiogenesis and invasion by modifying these angiogenic and invasive markers. The finding of the present study was further confirmed by molecular docking analysis that shows a strong binding interaction between AITC with STAT-3 and cocrystal structure of STAT-3 glide energy of −18.123 and −72.246 (kcal/mole), respectively. Overall, the results suggested that AITC inhibits activation of the JAK-1/STAT-3 pathway, which subsequently prevents angiogenesis and invasion. It was recommended that AITC might develop a beneficial effect against breast cancer.
Sweroside: An iridoid glycoside of potential neuroprotective, antidiabetic, and antioxidant activities supported by molecular docking
Amino Acids ( IF 3.789 ) Pub Date : 2023-03-20 , DOI: 10.1007/s00726-023-03262-9
GokhanZengin,MohamedEl-Raey,WalaaEl-Kashak,GaberEl-SaberBatiha,DuaaAlthumairy,SarahAlamer,NadaM.Mostafa,OmaymaA.Eldahshan
Oxidative stress can be a series burden on human health and may lead to many chronic diseases such as diabetes and neurological disorders. The use of natural products to scavenge the reactive oxygen species has attracted the attention of many researchers, to safely manage these conditions with fewer side effects, in available and cost-effective ways. The current study aimed at the isolation and structure elucidation of sweroside from Schenkia spicata (Gentianaceae) and the evaluation of its antioxidant, antidiabetic, neuroprotective, and enzyme inhibitory potential via in vitro and in silico studies. The antioxidant potential was evaluated by a variety of assays as ABTS, CUPRAC and FRAP, showing values of 0.34 ± 0.08, 21.14 ± 0.43, and 12.32 ± 0.20 mg TE/g, respectively, while demonstrating 0.75 ± 0.03 mmol TE/g for phosphomolybdenum (PBD) assay. Acetylcholinestrase (AChE), butyrylcholinesterase (BChE) and tyrosinase inhibitory activities were used to evaluate the neuroprotective effect, while the antidiabetic potential was evaluated by measuring α-amylase and glucosidase inhibitory activities. Results revealed that sweroside showed antioxidant and inhibitory effects on the enzymes tested with the exception of AChE. It demonstrated good tyrosinase inhibitory ability with 55.06 ± 1.85 mg Kojic acid equivalent /g. Regarding the antidiabetic ability, the compound displayed both amylase and glucosidase (0.10 ± 0.01 and 1.54 ± 0.01 mmol Acarbose equivalent/g, respectively) inhibitory activities. Molecular docking studies of sweroside on the active sites of the aforementioned enzymes in addition to NADPH oxidase were performed using Discovery Studio 4.1 software. Results revealed good binding affinities of sweroside to these enzymes mainly through hydrogen bonds and van der Waals interactions. Sweroside can be an important antioxidant and enzyme inhibitory supplement, yet further in vivo and clinical studies are required.
Development of peptide-based biosensors for detecting cross-linking and deamidation activities of transglutaminases
Amino Acids ( IF 3.789 ) Pub Date : 2023-05-10 , DOI: 10.1007/s00726-023-03272-7
HidekiTatsukawa,RurikoAoyama,KiyotakaHitomi
Transglutaminases (TGs) are a protein family that catalyzes isopeptide bond formation between glutamine and lysine residues of various proteins. There are eight TG isozymes in humans, and each is involved in diverse biological phenomena due to their characteristic distribution. Abnormal activity of TG1 and TG2, which are major TG isozymes, is believed to cause various diseases, such as ichthyosis and celiac disease. To elucidate TGs’ mechanisms of action and develop new therapeutic strategies, it is essential to develop bioprobes that can specifically examine the activity of each TG isozyme, which has not been sufficiently studied. We previously have identified several substrate peptide sequences containing Gln residues for each isozyme and developed a method to detect isozyme-specific activities by incorporating a labeled substrate peptide into lysine residues of proteins. We prepared the fluorescein isothiocyanate (FITC)-labeled Gln substrate peptide (FITC-K5 and FITC-T26) and Rhodamine B-labeled Lys substrate peptide (RhoB-Kpep). Each TG reaction specifically cross-linked these probe pairs, and the proximity of FITC and Rhodamine B significantly decreased the fluorescence intensity of FITC depending on the concentration and reaction time of each TG. In this study, we developed a peptide-based biosensor that quickly and easily measures TG isozyme-specific activity. This probe is expected to be helpful in elucidating TG’s physiological and pathological functions and in developing compounds that modulate TG activity.
Association between the antioxidant properties of SESN proteins and anti-cancer therapies
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-07 , DOI: 10.1007/s00726-023-03281-6
JoannaKozak,KatarzynaJonak
Since the beginning of SESN protein development, they have attracted highly progressive attention due to their regulatory role in multiple signalling pathways. Through their antioxidant activity and autophagy regulation implication, they can function as powerful antioxidants to reduce oxidative stress in cells. SESN proteins received special attention in the field of regulation of reactive oxygen species level in the cell and its interplay with signalling pathways determining energy and nutrient homeostasis. Since perturbations in these pathways are implicated in cancer onset and development, SESNs might constitute potential novel therapeutic targets of broad interest. In this review, we discuss the impact of SESN proteins on anti-cancer therapy based on naturally occurring compounds and conventionally used drugs that influence oxidative stress and autophagy-induced cellular signalling pathways. The significant changes in reactive oxygen species level and nutrient status in cancer cells generate subsequent biological effect through the regulation of SESN-dependent pathways. Thus, SESN may serve as the key molecule for regulating anti-cancer drugs’ induced cellular response.
K-aurein: A notable aurein 1.2-derived peptide that modulates Candida albicans filamentation and reduces biofilm biomass
Amino Acids ( IF 3.789 ) Pub Date : 2023-07-13 , DOI: 10.1007/s00726-023-03288-z
MariaLaínaSilva,MariaNágilaCarneiro,RafaelaMesquitaBastosCavalcante,JesúsAlbertoPérezGuerrero,RaquelOliveiraSantosFontenelle,EstebanNicolásLorenzón,EduardoMaffudCilli,VictorAlvesCarneiro
Candida albicans is considered one of the most important opportunistic fungi due to the large arsenal of virulence factors that help throughout the progress of the infection. In this sense, antimicrobial peptides (AMPs) appear as an alternative, with great antifungal action. Among these, aurein 1.2 has been widely explored, becoming the basis for the discovery of new AMPs, such as K-aurein (K-au). Thus, this study evaluated the anti-C. albicans potential of K-au against virulence factors, planktonic growth, and biofilm formation of clinical isolates. Firstly, K-au antifungal activity was determined by the microdilution method and time-kill curve. The inhibition of hydrolytic enzyme secretion (proteinase, phospholipase, and hemolysin) and germ tube formation was tested. Then, the antibiofilm potential of K-au was verified through biomass quantification and scanning electron microscopy (SEM). All tests were compared with the classical antifungal drug, amphotericin B (AmB). The outcomes showed fungicidal action of K-au at 62.50 µg mL−1 for all isolates, with a time of action around 150–180 min, determined by the time-kill curve. K-au-treated cells decreased by around 40% of the germinative tube compared to the control. Additionally, K-au inhibited the biofilm formation by more than 90% compared to AmB and the control group. SEM images show apparent cellular disaggregation without the formation of filamentous structures. Therefore, the findings suggest a promising anti-C. albicans effect of K-au due to its fungicidal activity against planktonic cells, or its ability to inhibit important virulence factors like germ tube and biofilm formation. Thus, this peptide could be explored as a useful compound against C. albicans-related infection.
Insights into the synthesis strategies of plant-derived cyclotides
Amino Acids ( IF 3.789 ) Pub Date : 2023-05-04 , DOI: 10.1007/s00726-023-03271-8
ThaoNTHo,SonHPham,LinhTTNguyen,HaTNguyen,LuanTNguyen,TienTDang
Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure–activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes.
Plasma free amino acid profiles are associated with serum high molecular weight adiponectin levels in Japanese medical check-up population without type 2 diabetes mellitus
Amino Acids ( IF 3.789 ) Pub Date : 2023-03-17 , DOI: 10.1007/s00726-023-03257-6
KengoTokunaga,HidehiroNakamura,SakinoToue,YumikoKato,YosukeIda,SawakoMiyoshi,RikaYoneyama,HiroakiOhnishi,TadakazuHisamatsu,SusumuOkamoto
To prevent the progression of type 2 diabetes mellitus (T2DM), early detection and intervention are important. Several studies have already shown that the serum adiponectin level could be useful for evaluating the future risk of T2DM. Recently, plasma free amino acid (PFAA) concentrations have also emerged as potential biomarkers that predict the future onset of T2DM. In this study, we aimed to further characterise PFAA profiles by elucidating the association with the serum high molecular weight (HMW) adiponectin level in this cross-sectional study. A total of 1000 Japanese subjects who underwent medical check-ups were enrolled, and their plasma concentrations of 21 amino acids and clinical parameters were measured. The subjects without T2DM were divided into quartiles (Q1-4) by serum HMW adiponectin level, and the association with between PFAA concentrations was analysed. Concentrations of glutamate, alanine, proline, tyrosine, histidine, methionine, lysine, branched-chain amino acids (BCAAs) and tryptophan varied significantly according to the adiponectin quartile. Furthermore, serum adiponectin levels showed significant inverse correlations with these amino acids. The change in the PFAA profile in the group with the lowest adiponectin concentrations (Q1) was similar to that of T2DM patients. Although both adiponectin levels and PFAA concentrations are known to be altered by the accumulation of visceral fat and insulin resistance, the levels of glutamate, BCAA, lysine and tryptophan remain significantly associated with adiponectin level after adjustment for age, body mass index and homeostasis model assessment of insulin resistance, showing the direct association between PFAA concentrations and the serum HMW adiponectin level. Registration number: University Hospital Medical Information Network Clinical Trials Registry (UMIN-CTR) UMIN000029920, registered on Nov 13th 2017 (prospectively registered).
In the quest for histone deacetylase inhibitors: current trends in the application of multilayered computational methods
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-27 , DOI: 10.1007/s00726-023-03297-y
AbdullahiIbrahimUba,GokhanZengin
Histone deacetylase (HDAC) inhibitors have gained attention over the past three decades because of their potential in the treatment of different diseases including various forms of cancers, neurodegenerative disorders, autoimmune, inflammatory diseases, and other metabolic disorders. To date, 5 HDAC inhibitor drugs are marketed for the treatment of hematological malignancies and several drug-candidate HDAC inhibitors are at different stages of clinical trials. However, due to the toxic side effects of these drugs resulting from the lack of target selectivity, active studies are ongoing to design and develop either class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure–activity relationships (3D-QSAR); and structure-based virtual screening (molecular docking). The current trends involve the application of the combination of these methods and incorporating molecular dynamics simulations coupled with Poisson–Boltzmann/molecular mechanics generalized Born surface area (MM-PBSA/MM-GBSA) to improve the prediction of ligand binding affinity. This review aimed at understanding the current trends in applying these multilayered strategies and their contribution to the design/identification of HDAC inhibitors.
Mouse skin peptidomic analysis of the hemorrhage induced by a snake venom metalloprotease
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-30 , DOI: 10.1007/s00726-023-03299-w
AmandaFAsega,BiancaCSCBarros,AlisonFAChaves,AnaKOliveira,LucianaBertholim,EduardoSKitano,SolangeMTSerrano
Hemorrhage induced by snake venom metalloproteases (SVMPs) results from proteolysis, capillary disruption, and blood extravasation. HF3, a potent SVMP of Bothrops jararaca, induces hemorrhage at pmol doses in the mouse skin. To gain insight into the hemorrhagic process, the main goal of this study was to analyze changes in the skin peptidome generated by injection of HF3, using approaches of mass spectrometry-based untargeted peptidomics. The results revealed that the sets of peptides found in the control and HF3-treated skin samples were distinct and derived from the cleavage of different proteins. Peptide bond cleavage site identification in the HF3-treated skin showed compatibility with trypsin-like serine proteases and cathepsins, suggesting the activation of host proteinases. Acetylated peptides, which originated from the cleavage at positions in the N-terminal region of proteins in both samples, were identified for the first time in the mouse skin peptidome. The number of peptides acetylated at the residue after the first Met residue, mostly Ser and Ala, was higher than that of peptides acetylated at the initial Met. Proteins cleaved in the hemorrhagic skin participate in cholesterol metabolism, PPAR signaling, and in the complement and coagulation cascades, indicating the impairment of these biological processes. The peptidomic analysis also indicated the emergence of peptides with potential biological activities, including pheromone, cell penetrating, quorum sensing, defense, and cell–cell communication in the mouse skin. Interestingly, peptides generated in the hemorrhagic skin promoted the inhibition of collagen-induced platelet aggregation and could act synergistically in the local tissue damage induced by HF3.
Biocidal and antibiofilm activities of arginine-based surfactants against Candida isolates
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-29 , DOI: 10.1007/s00726-023-03296-z
MElisaFait,PatriciaDGrillo,GracielaLGarrote,EduardoDPrieto,RominaFVázquez,MarioCNSaparrat,SusanaRMorcelle
Amino-acid-based surfactants are a group of compounds that resemble natural amphiphiles and thus are expected to have a low impact on the environment, owing to either the mode of surfactant production or its means of disposal. Within this context, arginine-based tensioactives have gained particular interest, since their cationic nature—in combination with their amphiphilic character—enables them to act as broad-spectrum biocides. This capability is based mainly on their interactive affinity for the microbial envelope that alters the latter’s structure and ultimately its function. In the work reported here, we investigated the efficiency of Nα-benzoyl arginine decyl- and dodecylamide against Candida spp. to further our understanding of the antifungal mechanism involved. For the assays, both a Candida albicans and a Candida tropicalis clinical isolates along with a C. albicans–collection strain were used as references. As expected, both arginine-based compounds proved to be effective against the strains tested through inhibiting both the planktonic and the sessile growth. Furthermore, atomic force microscopy techniques and lipid monolayer experiments enabled us to gain insight into the effect of the surfactant on the cellular envelope. The results demonstrated that all the yeasts treated exhibited changes in their exomorphologic structure, with respect to alterations in both roughness and stiffness, relative to the nontreated ones. This finding—in addition to the amphiphiles’ proven ability to insert themselves within this model fungal membrane—could explain the changes in the yeast-membrane permeability that could be linked to viability loss and mixed-vesicle release.
ACP-Dnnel: anti-coronavirus peptides’ prediction based on deep neural network ensemble learning
Amino Acids ( IF 3.789 ) Pub Date : 2023-07-04 , DOI: 10.1007/s00726-023-03300-6
MingyouLiu,HongmeiLiu,TaoWu,YingxueZhu,YuweiZhou,ZiruHuang,ChangchengXiang,JianHuang
The ongoing COVID-19 pandemic has caused dramatic loss of human life. There is an urgent need for safe and efficient anti-coronavirus infection drugs. Anti-coronavirus peptides (ACovPs) can inhibit coronavirus infection. With high-efficiency, low-toxicity, and broad-spectrum inhibitory effects on coronaviruses, they are promising candidates to be developed into a new type of anti-coronavirus drug. Experiment is the traditional way of ACovPs’ identification, which is less efficient and more expensive. With the accumulation of experimental data on ACovPs, computational prediction provides a cheaper and faster way to find anti-coronavirus peptides’ candidates. In this study, we ensemble several state-of-the-art machine learning methodologies to build nine classification models for the prediction of ACovPs. These models were pre-trained using deep neural networks, and the performance of our ensemble model, ACP-Dnnel, was evaluated across three datasets and independent dataset. We followed Chou's 5-step rules. (1) we constructed the benchmark datasets data1, data2, and data3 for training and testing, and introduced the independent validation dataset ACVP-M; (2) we analyzed the peptides sequence composition feature of the benchmark dataset; (3) we constructed the ACP-Dnnel model with deep convolutional neural network (DCNN) merged the bi-directional long short-term memory (BiLSTM) as the base model for pre-training to extract the features embedded in the benchmark dataset, and then, nine classification algorithms were introduced to ensemble together for classification prediction and voting together; (4) tenfold cross-validation was introduced during the training process, and the final model performance was evaluated; (5) finally, we constructed a user-friendly web server accessible to the public at http://150.158.148.228:5000/. The highest accuracy (ACC) of ACP-Dnnel reaches 97%, and the Matthew’s correlation coefficient (MCC) value exceeds 0.9. On three different datasets, its average accuracy is 96.0%. After the latest independent dataset validation, ACP-Dnnel improved at MCC, SP, and ACC values 6.2%, 7.5% and 6.3% greater, respectively. It is suggested that ACP-Dnnel can be helpful for the laboratory identification of ACovPs, speeding up the anti-coronavirus peptide drug discovery and development. We constructed the web server of anti-coronavirus peptides’ prediction and it is available at http://150.158.148.228:5000/.
A new 68Ga-labeled ornithine derivative for PET imaging of ornithine metabolism in tumors
Amino Acids ( IF 3.789 ) Pub Date : 2023-02-21 , DOI: 10.1007/s00726-023-03250-z
HongliangWang,KaixinQin,DongmeiShi,PingWu,XinzhongHao,HaiyanLiu,JieGao,JianguoLi,ZhifangWu,SijinLi
Ornithine metabolism plays a vital role in tumorigenesis. For cancer cells, ornithine is mainly used as a substrate for ornithine decarboxylase (ODC) for the synthesis of polyamines. The ODC as a key enzyme of polyamine metabolism has become an important target for cancer diagnosis and treatment. To non-invasively detect the levels of ODC expression in malignant tumors, we have synthesized a novel 68Ga-labeled ornithine derivative ([68Ga]Ga-NOTA-Orn). The synthesis time of [68Ga]Ga-NOTA-Orn was about 30 min with a radiochemical yield of 45–50% (uncorrected), and the radiochemical purity was > 98%. [68Ga]Ga-NOTA-Orn was stable in saline and rat serum. Cellular uptake and competitive inhibition assays using DU145 and AR42J cells demonstrated that the transport pathway of [68Ga]Ga-NOTA-Orn was similar to that of l-ornithine, and it could interact with the ODC after transporting into the cell. Biodistribution and micro-positron emission tomography (Micro-PET) imaging studies showed that [68Ga]Ga-NOTA-Orn exhibited rapid tumor uptake and was rapidly excreted through the urinary system. All above results suggested that [68Ga]Ga-NOTA-Orn is a novel amino acid metabolic imaging agent with great potential of tumor diagnosis.
Acetyl group for proper protection of β-sugar-amino acids used in SPPS
Amino Acids ( IF 3.789 ) Pub Date : 2023-06-21 , DOI: 10.1007/s00726-023-03278-1
IstvánVarga,ViktóriaGoldschmidtGőz,IstvánPintér,AntalCsámpai,AndrásPerczel
The synthesis of d-glucosamine-1-carboxylic acid based β-sugar amino acids (β-SAAs) is typically performed in nine consecutive steps via an inefficient OAc → Br → CN conversion protocol with low overall yield. Here, we present the improved and more efficient synthesis of both Fmoc-GlcAPC-OH and Fmoc-GlcAPC(Ac)-OH, β-SAAs consisting of only 4–5 synthetic steps. Their active ester and amide bond formation with glycine methyl ester (H-Gly-OMe) was completed and monitored by 1H NMR. The stability of the pyranoid OHs protecting the acetyl groups was investigated under three different Fmoc cleavage conditions and was found to be satisfactory even at high piperidine concentration (e.g. 40%). We designed a SPPS protocol using Fmoc-GlcAPC(Ac)-OH to produce model peptides Gly-β-SAA-Gly as well as Gly-β-SAA-β-SAA-Gly with high coupling efficiency. The products were deacetylated using the Zemplén method, which allows the hydrophilicity of a building block and/or chimera to be fine-tuned, even after the polypeptide chain has already been synthesized.
Correction to: The association of fasting plasma thiol fractions with body fat compartments, biomarker profile, and adipose tissue gene expression
Amino Acids ( IF 3.789 ) Pub Date : 2023-02-16 , DOI: 10.1007/s00726-023-03244-x
AmanyElshorbagy,NasserEBastani,SindreLee-Ødegård,BenteØvrebø,NadiaHaj-Yasein,KarianneSvendsen,CherylTurner,HelgaRefsum,KathrineJVinknes,ThomasOlsen
Chromogranin A-derived peptides pancreastatin and catestatin: emerging therapeutic target for diabetes
Amino Acids ( IF 3.789 ) Pub Date : 2023-03-13 , DOI: 10.1007/s00726-023-03252-x
RichaGarg,ArunAgarwal,RoshanKatekar,ShaileshDadge,ShubhiYadav,JiaurRGayen
Chromogranin A (ChgA) is an acidic pro-protein found in neuroendocrine organs, pheochromocytoma chromaffin granules, and tumor cells. Proteolytic processing of ChgA gives rise to an array of biologically active peptides such as pancreastatin (PST), vasostatin, WE14, catestatin (CST), and serpinin, which have diverse roles in regulating cardiovascular functions and metabolism, as well as inflammation. Intricate tissue-specific role of ChgA-derived peptide activity in preclinical rodent models of metabolic syndrome reveals complex effects on carbohydrate and lipid metabolism. Indeed, ChgA-derived peptides, PST and CST, play a pivotal role in metabolic syndrome such as obesity, insulin resistance, and diabetes mellitus. Additionally, supplementation of specific peptide in ChgA-KO mice have an opposing effect on physiological functions, such as PST supplementation reduces insulin sensitivity and enhances inflammatory response. In contrast, CST supplementation enhances insulin sensitivity and reduces inflammatory response. In this review, we focus on the tissue-specific role of PST and CST as therapeutic targets in regulating carbohydrate and lipid metabolism, along with the associated risk factors.
The biological interactions between kynurenine and AhR in melanocytes: in vitro studies
Amino Acids ( IF 3.789 ) Pub Date : 2023-05-28 , DOI: 10.1007/s00726-023-03279-0
KatarzynaWalczak,KarolinaSzalast,DorotaKrasowska
Kynurenine (KYN), a tryptophan metabolite, is endogenously produced by the skin cells and is present in human sweat. The aim of this study was to determine the molecular mechanism of the antiproliferative activity of KYN on human epidermal melanocytes. KYN significantly inhibited the metabolic activity of HEMa cells by decreasing cyclin D1 and cyclin-dependent kinase 4 (CDK4) levels via the aryl hydrocarbon receptor (AhR) pathway. The results suggested that KYN might be involved in the regulation of physiological and pathological processes mediated by melanocytes.
中科院SCI期刊分区
大类学科小类学科TOP综述
生物3区BIOCHEMISTRY & MOLECULAR BIOLOGY 生化与分子生物学3区
补充信息
自引率H-indexSCI收录状况PubMed Central (PML)
6.0092Science Citation Index Science Citation Index Expanded
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Amino Acids publishes contributions from all fields of amino acid and protein research: analysis, separation, synthesis, biosynthesis, cross linking amino acids, racemization/enantiomers, modification of amino acids as phosphorylation, methylation, acetylation, glycosylation and nonenzymatic glycosylation, new roles for amino acids in physiology and pathophysiology, biology, amino acid analogues and derivatives, polyamines, radiated amino acids, peptides, stable isotopes and isotopes of amino acids. Applications in medicine, food chemistry, nutrition, gastroenterology, nephrology, neurochemistry, pharmacology, excitatory amino acids are just some topics to be listed. We also encourage the submission of papers of interdisciplinary borderlines.Fields of interest: Biochemistry, food chemistry, nutrition, neurology, psychiatry, pharmacology, nephrology, gastroenterology, microbiology