Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis.

Capreomycin (CMN) and viomycin (VIO) are nonribosomal peptide antituberculosis antibiotics, the structures of which contain four nonproteinogenic amino acids, including l-2,3-diaminopropionic acid (l-Dap), ß-ureidodehydroalanine, l-capreomycidine, and ß-lysine. Previous bioinformatics analysis suggested that CmnB/VioB and CmnK/VioK participate in the formation of l-Dap; however, the real substrates of these enzymes are yet to be confirmed. We herein show that starting from O-phospho-l-Ser (OPS) and l-Glu precursors, CmnB catalyzes the condensation reaction to generate a metabolite intermediate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid (ACEGA), which undergoes NAD+-dependent oxidative hydrolysis by CmnK to generate l-Dap. Furthermore, the binding site of ACEGA and the catalytic mechanism of CmnK were elucidated with the assistance of three crystal structures, including those of apo-CmnK, the NAD+-CmnK complex, and CmnK in an alternative conformation. The CmnK-ACEGA docking model revealed that the glutamate α-hydrogen points toward the nicotinamide moiety. It provides evidence that the reaction is dependent on hydride transfer to form an imine intermediate, which is subsequently hydrolyzed by a water molecule to produce l-Dap. These findings modify the original proposed pathway and provide insights into l-Dap formation in the biosynthesis of other related natural products.

High-Rate Hydrogen Generation by Direct Sunlight Irradiation with a Triruthenium Complex.

Herein we report a biomimetic triruthenium catalyst that, when under direct sunlight irradiation, facilitates high-rate H2 production from formic acid (FA) dehydrogenation. The system consists of 2 µmol of catalyst and 6 µmol of tri- o-tolylphosphine in 1 mL of dimethylformamide (DMF) and 4 mL of FA/triethylamine (TEA; 5:2). With 0.4 mM catalyst loaded, a high turnover frequency of 1.15 × 106 h-1 was detected when under direct sunlight irradiation. In an experiment with 0.2 mM catalyst loaded, more than 140 L of H2 (280 L of H2 + CO2) was produced, and a turnover number of approximately 2.78 × 106 was obtained within 5 h without decline in H2 generation activity, making it suitable for high-rate H2 production.

Characterization and epitope mapping of Dengue virus type 1 specific monoclonal antibodies.

BACKGROUND: Dengue virus (DV) infection causes a spectrum of clinical diseases ranging from dengue fever to a life-threatening dengue hemorrhagic fever. Four distinct serotypes (DV1-4), which have similar genome sequences and envelope protein (E protein) antigenic properties, were divided. Among these 4 serotypes, DV1 usually causes predominant infections and fast diagnosis and effective treatments are urgently required to prevent further hospitalization and casualties. METHODS: To develop antibodies specifically targeting and neutralizing DV1, we immunized mice with UV-inactivated DV1 viral particles and recombinant DV1 E protein from residue 1 to 395 (E395), and then generated 12 anti-E monoclonal antibodies (mAbs) as the candidates for a series of characterized assays such as ELISA, dot blot, immunofluorescence assay, western blot, and foci forming analyses. RESULTS: Among the mAbs, 10 out of 12 showed cross-reactivity to four DV serotypes as well as Japanese encephalitis virus (JEV) in different cross-reactivity patterns. Two particular mAbs, DV1-E1 and DV1-E2, exhibited strong binding specificity and neutralizing activity against DV1 and showed no cross-reactivity to DV2, DV3, DV4 or JEV-infected cells as characterized by ELISA, dot blot, immunofluorescence assay, western blot, and foci forming analyses. Using peptide coated indirect ELISA, we localized the neutralizing determinants of the strongly inhibitory mAbs to a sequence-unique epitope on the later-ridge of domain III of the DV1 E protein, centered near residues T346 and D360 (346TQNGRLITANPIVTD360). Interestingly, the amino acid sequence of the epitope region is highly conserved among different genotypes of DV1 but diverse from DV2, DV3, DV4 serotypes and other flaviviruses. CONCLUSIONS: Our results showed two selected mAbs DV1-E1 and DV1-E2 can specifically target and significantly neutralize DV1. With further research these two mAbs might be applied in the development of DV1 specific serologic diagnosis and used as a feasible treatment option for DV1 infection. The identification of DV1 mAbs epitope with key residues can also provide vital information for vaccine design.

Potential antitumor therapeutic application of Grimontia hollisae thermostable direct hemolysin mutants.

We report on the preparation of a new type of immunotoxin by conjugation of an epidermal growth factor receptor (EGFR)-binding peptide and an R46E mutation of thermostable direct hemolysin from Grimontia hollisae, (Gh-TDH(R) (46E) /EB). The hybrid immunotoxin was purified to homogeneity and showed a single band with slight slower mobility than that of Gh-TDH(R) (46E) . Cytotoxicity assay of Gh-TDH(R) (46E) /EB on EGFR highly, moderately, low, and non-expressed cells, A431, MDA-MB-231, HeLa, and HEK293 cells, respectively, showed apparent cytotoxicity on A431 and MDA-MB-231 cells but not on HeLa or HEK293 cells. In contrast, no cytotoxicity was observed for these cells treated with either Gh-TDH(R) (46E) or EB alone, indicating enhanced cytotoxic efficacy of Gh-TDH(R) (46E) by the EGFR binding moiety. Further antitumor activity assay of Gh-TDH(R) (46E) /EB in a xenograft model of athymic nude mice showed obvious shrinkage of tumor size and degeneration, necrosis, and lesions of tumor tissues compared to the normal tissues. Therefore, the combination of Gh-TDH(R) (46E) with target affinity agents opens new possibilities for pharmacological treatment of cancers and potentiates the anticancer drug's effect.

A ruthenium-based biomimetic hydrogen cluster for efficient photocatalytic hydrogen generation from formic acid.

A ruthenium-based biomimetic hydrogen cluster, [Ru2 (CO)6 (µ-SCH2 CH2 CH2 S)] (1), has been synthesized and, in the presence of the P ligand tri(o-tolyl)phosphine, demonstrated efficient photocatalytic hydrogen generation from formic acid decomposition. Turnover frequencies (TOFs) of 5500 h(-1) and turnover numbers (TONs) over 24 700 were obtained with less than 50 ppm of the catalyst, thus representing the highest TOFs for ruthenium complexes as well as the best efficiency for photocatalytic hydrogen production from formic acid. Moreover, 1 showed high stability with no significant degradation of the photocatalyst observed after prolonged photoirradiation at 90 °C.

Effects of fermentation on antioxidant properties and phytochemical composition of soy germ.

BACKGROUND: Traditional soy-fermented foods, such as miso, douche, natto, and tempeh have been widely used as a dietary supplement in Asian countries, and numerous reports on their phenolics and antioxidant activities have been published. Soy germ contains 10-fold higher phenolics than whole soybean, hence using soy germ as fermentation substrate will be more efficient than whole soybean. RESULTS: Soy germ fermented with Aspergillus niger M46 resulted in a high-efficiency bio-transformation of phenolics and flavonoids to their metabolites, and a diverse secondary metabolic product was also found to response oxidation stress of fungal colonisation. Its antioxidant activity against hydroxyl radicals and superoxide radicals (IC50 = 0.8 and 6.15 µg mL(-1) , respectively) was about 205-fold and 47-fold higher than those of unfermented soy germ (IC50 = 164.0 and 290.48 µg mL(-1) ), respectively. These results were similar to those observed for Trolox, and more active than those of BHT and hesperidin. The ß-glucosidase and α-amylase produced during fermentation were mainly responsible for mobilisation of the phenolics. CONCLUSION: Our results demonstrate that fermented soy germ has the potential to be a good dietary supplement for prevention of oxidative stress-related diseases, and the solid-state bioprocessing strategy could be an innovative approach to enhance the antioxidant activity of soy germ.

Reconstitution of the early steps of gliotoxin biosynthesis in Aspergillus nidulans reveals the role of the monooxygenase GliC.

The gliotoxin, a member of the epipolythiodioxopiperazine (ETP), has received considerable attention from the scientific community for its wide range of biological activity. Despite the identification of gliotoxin cluster, however, the sequence of steps in the gliotoxin biosynthesis has remained elusive. As an alternative to the gene knock-out and biochemical approaches used so far, here we report using a heterologous expression approach to determine the sequence of the early steps of gliotoxin biosynthesis in Aspergillus nidulans. We identified the GliC, a monooxygenases that involved in the second step of gliotoxin biosynthesis pathway through the catalyzing the hydroxylation at the α-position of L-Phe.

Protein engineering of oxidosqualene-lanosterol cyclase into triterpene monocyclase.

A computational modeling/protein engineering approach was applied to probe H234, C457, T509, Y510, and W587 within Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase (ERG7), which spatially affects the C-10 cation of lanosterol formation. Substitution of Trp587 to aromatic residues supported the "aromatic hypothesis" that the π-electron-rich pocket is important for the stabilization of electron-deficient cationic intermediates. The Cys457 to Gly and Thr509 to Gly mutations disrupted the pre-existing H-bond to the protonating Asp456 and the intrinsic His234 : Tyr510 H-bond network, respectively, and generated achilleol A as the major product. An H234W/Y510W double mutation altered the ERG7 function to achilleol A synthase activity and generated achilleol A as the sole product. These results support the concept that a few-ring triterpene synthase can be derived from polycyclic cyclases by reverse evolution, and exemplify the power of computational modeling coupled with protein engineering both to study the enzyme's structure-function-mechanism relationships and to evolve new enzymatic activity.

Solution-Processable Donor-Acceptor Copolymer Thin Films for Efficient Visible-Light-Driven Photocatalytic Hydrogen Evolution.

Conjugated polymers (CPs) have been actively utilized as photocatalysts for hydrogen evolution due to their easy synthetic tunability to endow specific functionalities, including visible-light absorption, higher-lying LUMO energy for proton reduction, and sufficient photochemical stability. Enhancing interfacial surface and compatibility of hydrophobic CPs with hydrophilic water is the central focus to improve the hydrogen evolution rate (HER). Although a number of successful approaches have been developed in recent years, tedious chemical modifications or post-treatment of CPs make reproducibility of the materials difficult. In this work, a solution processable PBDB-T polymer is directly deposited on a glass substrate to form a thin film that is immersed in an aqueous solution to photochemically catalyze H2 generation. The PBDB-T thin film showed a much higher hydrogen evolution rate (HER) than the typical method of using PBDB-T suspended solids due to the enhanced interfacial area with a more suitable solid-state morphology. When the thickness of the thin film is reduced to dramatically improve the utilization of the photocatalytic material, the 0.1 mg-based PBDB-T thin film exhibited an unprecedentedly high HER of 120.90 mmol h-1 g-1.

Quinazolinone-Peptido-Nitrophenyl-Derivatives as Potential Inhibitors of SARS-CoV-2 Main Protease.

The severe acute respiratory syndrome coronavirus 2 main protease (SARS-CoV-2-Mpro) plays an essential role in viral replication, transcription, maturation, and entry into host cells. Furthermore, its cleavage specificity for viruses, but not humans, makes it a promising drug target for the treatment of coronavirus disease 2019 (COVID-19). In this study, a fragment-based strategy including potential antiviral quinazolinone moiety and glutamine- or glutamate-derived peptidomimetic backbone and positioned nitro functional groups was used to synthesize putative Mpro inhibitors. Two compounds, G1 and G4, exhibited anti-Mpro enzymatic activity in a dose-dependent manner, with the calculated IC50 values of 22.47 ± 8.93 µM and 24.04 ± 0.67 µM, respectively. The bio-layer interferometer measured real-time binding. The dissociation kinetics of G1/Mpro and G4/Mpro also showed similar equilibrium dissociation constants (KD) of 2.60 × 10-5 M and 2.55 × 10-5 M, respectively, but exhibited distinct association/dissociation curves. Molecular docking of the two compounds revealed a similar binding cavity to the well-known Mpro inhibitor GC376, supporting a structure-function relationship. These findings may open a new avenue for developing new scaffolds for Mpro inhibition and advance anti-coronavirus drug research.

Crystal structure and inhibition studies of transglutaminase from Streptomyces mobaraense.

The crystal structure of the microbial transglutaminase (MTGase) zymogen from Streptomyces mobaraense has been determined at 1.9-Å resolution using the molecular replacement method based on the crystal structure of the mature MTGase. The overall structure of this zymogen is similar to that of the mature form, consisting of a single disk-like domain with a deep active cleft at the edge of the molecule. A major portion of the prosequence (45 additional amino acid residues at the N terminus of the mature transglutaminase) folds into an L-shaped structure, consisting of an extended N-terminal segment linked with a one-turn short helix and a long α-helix. Two key residues in the short helix of the prosequence, Tyr-12 and Tyr-16, are located on top of the catalytic triad (Cys-110, Asp-301, and His-320) to block access of the substrate acyl donors and acceptors. Biochemical characterization of the mature MTGase, using N-α-benzyloxycarbonyl-L-glutaminylglycine as a substrate, revealed apparent K(m) and k(cat)/K(m) values of 52.66 mM and 40.42 mM(-1) min(-1), respectively. Inhibition studies using the partial prosequence SYAETYR and homologous sequence SQAETYR showed a noncompetitive inhibition mechanism with IC(50) values of 0.75 and 0.65 mM, respectively, but no cross-linking product formation. Nevertheless, the prosequence homologous oligopeptide SQAETQR, with Tyr-12 and Tyr-16 each replaced with Gln, exhibited inhibitory activity with the formation of the SQAETQR-monodansylcadaverine fluorophore cross-linking product (SQAETQR-C-DNS). MALDI-TOF tandem MS analysis of SQAETQR-C-DNS revealed molecular masses corresponding to those of (N)SQAETQ(C)-C-DNS and C-DNS-(N)QR(C) sequences, suggesting the incorporation of C-DNS onto the C-terminal Gln residue of the prosequence homologous oligopeptide. These results support the putative functional roles of both Tyr residues in substrate binding and inhibition.

Molecular genetic analysis reveals that a nonribosomal peptide synthetase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis.

Genome sequencing of Aspergillus species including Aspergillus nidulans has revealed that there are far more secondary metabolite biosynthetic gene clusters than secondary metabolites isolated from these organisms. This implies that these organisms can produce additional secondary metabolites, which have not yet been elucidated. The A. nidulans genome contains 12 nonribosomal peptide synthetase (NRPS), one hybrid polyketide synthase/NRPS, and 14 NRPS-like genes. The only NRPS-like gene in A. nidulans with a known product is tdiA, which is involved in terrequinone A biosynthesis. To attempt to identify the products of these NRPS-like genes, we replaced the native promoters of the NRPS-like genes with the inducible alcohol dehydrogenase (alcA) promoter. Our results demonstrated that induction of the single NRPS-like gene AN3396.4 led to the enhanced production of microperfuranone. Furthermore, heterologous expression of AN3396.4 in Aspergillus niger confirmed that only one NRPS-like gene, AN3396.4, is necessary for the production of microperfuranone.

Evaluation of RevX solution extract as a potential inhibitor of the main protease of SARS-CoV-2-In vitro study and molecular docking.

The main protease (Mpro) of SARS-CoV-2 is a protease necessary for viral polyprotein processing and maturation. Mpro cleaves the polypeptide sequence after the glutamine residues. There is no known cellular protease with this substrate specificity in humans; therefore, it is considered an attractive drug target. Previously, fermented sorghum extract RevX (trademark of Revolutrx INC.) solution significantly alleviated physical decline and complications in a patient with lung adenocarcinoma, suggesting the role of bioactive components in RevX solution. To further explore whether the bioactive components in RevX solution exhibit other biological activities, such as antiviral effects, we investigated its inhibitory effect on the Mpro of SARS-CoV-2 virus. We report herein that the solid extract of the RevX solution exhibits an efficacious Mpro inhibitory activity, with IC50 of 2.07 ± 0.38 µg/mL. Molecular docking of sterol-like components in the RevX extracts identified by MS shows that the three sterol-like molecules can bind to the active region of the GC376-Mpro complex, supporting the structure-function relationship. Combined with its ability to significantly alleviate the body's immunity decline and to inhibit the activity of SARS-CoV-2 Mpro, RevX solution may provide a possible alternative supportive treatment for patients with COVID-19.

Dual-Mechanism Confers Self-Resistance to the Antituberculosis Antibiotic Capreomycin.

Capreomycin (CMN) is an important second-line antituberculosis antibiotic isolated from Saccharothrix mutabilis subspecies capreolus. The gene cluster for CMN biosynthesis has been identified and sequenced, wherein the cph gene was annotated as a phosphotransferase likely engaging in self-resistance. Previous studies reported that Cph inactivates two CMNs, CMN IA and IIA, by phosphorylation. We, herein, report that (1) Escherichia coli harboring the cph gene becomes resistant to both CMN IIA and IIB, (2) phylogenetic analysis regroups Cph to a new clade in the phosphotransferase protein family, (3) Cph shares a three-dimensional structure akin to the aminoglycoside phosphotransferases with a high binding affinity (KD) to both CMN IIA and IIB at micromolar levels, and (4) Cph utilizes either ATP or GTP as a phosphate group donor transferring its γ-phosphate to the hydroxyl group of CMN IIA. Until now, Cph and Vph (viomycin phosphotransferase) are the only two known enzymes inactivating peptide-based antibiotics through phosphorylation. Our biochemical characterization and structural determination conclude that Cph confers the gene-carrying species resistance to CMN by means of either chemical modification or physical sequestration, a naturally manifested belt and braces strategy. These findings add a new chapter into the self-resistance of bioactive natural products, which is often overlooked while designing new bioactive molecules.

Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from Vibrio alginolyticus reveal a new architecture of M20 metallopeptidases.

Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including L-carnosine and L-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD(CAT). The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an "extra" domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD(CAT) exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD(CAT) for GABAergic therapies or neuroprotection.

Mutation of isoleucine 705 of the oxidosqualene-lanosterol cyclase from Saccharomyces cerevisiae affects lanosterol's C/D-ring cyclization and 17α/ß-exocyclic side chain stereochemistry.

Site-saturated substitution in Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase at Ile705 position produced three chair-boat-chair (C-B-C) truncated tricyclic compounds, two 17α-exocyclic protosteryl intermediates, two protosteryl C-17 truncated rearranged intermediates and the normal biosynthetic product, lanosterol. These results indicated the importance of the Ile705 residue in affecting lanosterol's C/D ring stabilization including 6-6-5 tricyclic and protosteryl C-17 cations and 17α/ß-exocyclic side chain stereochemistry.

Purification, crystallization and preliminary X-ray analysis of a thermostable direct haemolysin from Grimontia hollisae.

Vibrio hollisae, a halophilic species recently reclassified as Grimontia hollisae, is a causative agent of gastroenteritis and septicaemia. One important pathogenic Vibrio factor, thermostable direct haemolysin (TDH), has been purified and crystallized in two crystal forms using the vapour-diffusion method. The crystals belonged to an orthorhombic space group, with unit-cell parameters a = 104.8, b = 112.4, c = 61.3 Šand a = 122.9, b = 123.3, c = 89.8 Å. The crystals contained either four or eight molecules per asymmetric unit, with predicted solvent contents of 49.4 and 46.3% and Matthews coefficients (V(M)) of 2.4 and 2.3 Å(3) Da(-1), respectively. These crystals were suitable for structure determination, which would yield structural details related to the cytotoxicity and oligomeric structure of this pore-forming toxin.

Predictive factors of the duration of a first-attack acute urticaria in children.

PURPOSES: This study's aim was to determine the predictive factors of the duration of first-attack acute urticaria in children. BASIC PROCEDURES: The sample included 1075 children admitted to the emergency department with first-attack acute urticaria. Variables comprising the clinical features and past histories of children with duration of disease of 3 days or less, 4 to 7 days, 8 to 14 days, and 15 days or more were compared to determine the predictors of duration of acute urticaria. MAIN FINDINGS: Age, various etiologies, clinical presentations, coexistent pyrexia or angioedema, and personal histories of allergic diseases were significant factors (all P < .05). Among allergic diseases, atopic dermatitis was the most significant predictor of duration of acute urticaria, and those with multiple allergic diseases had longer durations of urticaria (both P < .05). Oral plus injection forms of antihistamine or steroid were related to shorter duration of disease (P < .05). PRINCIPAL CONCLUSIONS: Etiologies and personal allergy history may be the most important predictors of the duration of a first attack of acute urticaria.

Significant factors associated with severity and outcome of an initial episode of acute urticaria in children.

The aim of this study was to determine the predictive factors of severity and duration of an initial episode of acute urticaria in children. This was a retrospective study of 1120 children of <18 yr who presented to the emergency department (ED) with an initial episode of acute urticaria during the period January 1, 2001, to December 31, 2007. These patients were followed in the ED or outpatient department (OPD) until their symptoms subsided. Variables comprising mild, moderate, and severe urticaria were compared to determine the predictors of severity. The relationships between duration of urticaria and clinical features, including physician-diagnosed causes and treatment modalities, were also analyzed. Significant predictive factors of severity of an initial episode of acute urticaria in children included age, physician-diagnosed causes of urticaria, clinical presentation, coexistent pyrexia or angioedema, and personal allergic history (all p < 0.001). The duration of urticaria was dependent on the physician-diagnosed causes and treatment. Inhalants and unknown causes were predictive of longer duration, while contact materials were associated with shorter duration of urticaria (p < 0.001). Combination treatment comprising an oral plus injectable form of antihistamine or corticosteroid significantly shortened the duration of urticaria compared to single treatment (p < 0.001), especially in children receiving short-term aggressive treatment in the pediatric observation unit (POU) of the ED.

Factors associated with sustained return of spontaneous circulation in children after out-of-hospital cardiac arrest of noncardiac origin.

PURPOSE: The study aimed to determine the factors predictive of sustained return of spontaneous circulation (ROSC) in children with out-of-hospital cardiac arrest (OHCA) of noncardiac origin. METHODS: Eighty children were included in this retrospective study. The variables that lead to sustained ROSC and those that do not lead to sustained ROSC were analyzed. Survival analyses, including chance of achieving sustained ROSC and sum duration of ROSC, were conducted according to the duration of in-hospital cardiopulmonary resuscitation (CPR). RESULTS: Etiologies of noncardiac OHCA differed significantly across different age groups (P < .001). Only 8.8% of children had initial arrest rhythms that were shockable. Predictors of sustained ROSC included the initial cardiac rhythm (P = .002), a shorter period between collapse and the first chest compression (P = .002), a shorter in-hospital CPR duration (P = .004), and prehospital CPR (P = .007). In children where ROSC was initially sustained, those with in-hospital CPR of more than 20 minutes, ROSC was sustained for less time (P < .001). CONCLUSIONS: Few children with noncardiac OHCA present with shockable cardiac rhythms. Furthermore, long-term ROSC is difficult to maintain in children who receive in-hospital CPR for more than 20 minutes.