Periselectivity and ambimodal transition states in cycloadditions of tetrachloro-o-benzoquinone with 6,6-dimethylfulvene.

The reaction mechanism of cycloadditions of tetrachloro-o-benzoquinone with 6,6-dimethylfulvene were systematically investigated with density functional theory calculations. It was found that conditional primary interactions stabilize the ambimodal transition states in the endo pathways. Ambimodal transition states lead to [6 + 4]/[4 + 2] adducts or [4 + 2]/[2 + 4] adducts, which interconvert through 3,3-sigmatropic shift reactions. The substituent effects on periselectivity were also investigated.

Fluoro, Trifluoromethyl, and Trifluoroacetyl Substituent Effects on Cycloaddition Reactivities: Computations and Analysis.

The importance of fluoro and trifluoromethyl substituents in drug effectiveness prompted the computational exploration of fluorine-containing substituents in valuable synthetic cycloadditions. Diels-Alder or 1,3-dipolar cycloaddition reactions of typical reactants, cyclopentadiene, N-phenyldiazoacetamide, tetrazine, and N-phenylsydnone involving fluorine-containing substituents (F, CF3, and COCF3) were studied with M06-2X density functional theory. Inductive and conjugative effects influence normal and inverse electron-demand reactions differently. These results provide a guide to the design and use of cycloadditions for the introduction of fluoro and trifluoromethyl substituents in synthetic processes.

Hydroximoyl fluorides as the precursors of nitrile oxides: synthesis, stability and [3 + 2]-cycloaddition with alkynes.

The transformation of hydroximoyl fluorides to nitrile oxides for [3 + 2]-cycloaddition with alkynes has been achieved for the first time. The hydroximoyl fluorides used in this work appeared to be not stable, which was proved by a series of experiments. A DFT calculation was performed to better understand the properties of hydroximoyl fluorides. Although not stable, the hydroximoyl fluorides could be successfully converted to the corresponding nitrile oxides for in situ [3 + 2]-cycloaddition with alkynes to yield the isoxazoles. Furthermore, it was feasible to conduct [3 + 2]-cycloaddition reaction without purification after the synthesis of hydroximoyl fluorides from gem-difluoroalkenes. By investigating a class of interesting yet previously rarely explored fluorinated compounds, this work sheds new light on the stability and reactivity of a C-F bond on a C[double bond, length as m-dash]N double bond.

Two isocitrate dehydrogenases from a plant pathogen Xanthomonas campestris pv. campestris 8004. Bioinformatic analysis, enzymatic characterization, and implication in virulence.

Isocitrate dehydrogenase (IDH) is a key enzyme in the tricarboxylate (TCA) cycle, which may play an important role in the virulence of pathogenic bacteria. Here, two structurally different IDHs from a plant pathogen Xanthomonas campestris pv. campestris 8004 (XccIDH1 and XccIDH2) were characterized in detail. The recombinant XccIDH1 forms homodimer in solution, while the recombinant XccIDH2 is a typical monomer. Phylogenetic analysis showed that XccIDH1 belongs to the type I IDH subfamily and XccIDH2 groups into the monomeric IDH clade. Kinetic characterization demonstrated that XccIDH1's specificity towards NAD(+) was 110-fold greater than NADP(+) , while XccIDH2's specificity towards NADP(+) was 353-fold greater than NAD(+) . The putative coenzyme discriminating amino acids (Asp268, Ile269 and Ala275 for XccIDH1, and Lys589, His590 and Arg601 for XccIDH2) were studied by site-directed mutagenesis. The coenzyme specificities of the two mutants, mXccIDH1 and mXccIDH2, were completely reversed from NAD(+) to NADP(+) , and NADP(+) to NAD(+) , respectively. Furthermore, Ser80 of XccIDH1, and Lys256 and Tyr421 of XccIDH2, were the determinants for the substrate binding. The detailed biochemical properties, such as optimal pH and temperature, thermostability, and metal ion effects, of XccIDH1 and XccIDH2 were further investigated. The possibility of taking the two IDHs into consideration as the targets for drug development to control the plant diseases caused by Xcc 8004 were described and discussed thoroughly.

Epidemiology and risk factors for nosocomial Non-Candida albicans candidemia in adult patients at a tertiary care hospital in North China.

Nosocomial candidemia extends the length of hospital stay, increases the costs of medical care, and is associated with a high mortality rate. Epidemiological data that assist in the choice of initial therapy may help to improve the prognosis. The present study was undertaken to investigate the epidemiology of nosocomial candidemia and identify risk factors for nosocomial candidemia caused by C. albicans and non-albicans Candida species (NAC). A retrospective chart review was undertaken to analyze cases of nosocomial candidemia treated at the Beijing Friendship Hospital between January 2008 and December 2012. All cases of candidemia were identified using the previously published criteria. Among 106 patients analyzed, 53.8% had nosocomial candidemia caused by NAC. Candida albicans was the most common causative agent, accounting for 46.2% of all cases, followed by C. glabrata (25.5%), C. tropicalis (15.1%), C. parapsilosis (10.4%) and C. Krusei (0.9%). Comparison of nosocomial C. albicans and NAC candidemia by multivariate logistic regression showed that factors independently associated with nosocomial NAC candidemia included exposure to azole agents (odds ratio [OR]: 3.359; 95% confidence interval [CI]: 1.136-10.154; P = .031) and artificial surgical implants (OR: 37.519; 95% CI: 2.5-562.998; P = .009). A significant risk factor for nosocomial C. albicans candidemia was cancer surgery (OR: 0.075; 95% CI: 0.013-0.437; P = .004). Clinical and epidemiological differences in the risk factors between nosocomial candidemia caused by C. albicans and NAC should be considered when selecting an initial antifungal regimen for the treatment of adult patients. This should be undertaken before the availability of species identification and/or antifungal susceptibility results.

Identification of a novel fumarase C from Streptomyces lividans TK54 as a good candidate for L-malate production.

Fumarase is a key enzyme that catalyzes the reversible hydration of fumarate to L-malate in the tricarboxylic acid cycle. This reaction has been extensively utilized for industrial applications in producing L-malate. In this study, a fumarase C gene from Streptomyces lividans TK54 (slFumC) was cloned and expressed as a fused protein (SlFumC) in Escherichia coli. The molecular mass of SlFumC was about 49 kDa determined by SDS-PAGE. Kinetic studies showed that the K m value of SlFumC for L-malate increased by approximately 8.5-fold at pH 6.5 (6.7 ± 0.81 mM) to 8.0 (57.0 ± 1.12 mM), which was higher than some known fumarases. The catalytic efficiency (k cat) and the specific activity increased by about 9.5-fold at pH 6.5 (65 s(-1)) to 8.0 (620 s(-1)) and from 79 U/mg at pH 6.5 to 752 U/mg at pH 8.0, respectively. Therefore, SlFumC may acquire strong catalytic ability by increasing pH to partially compensate for the loss of substrate affinity. The enzyme also showed substrate inhibition phenomenon, which is pH-dependent. Specific activity of SlFumC was gradually enhanced with increasing phosphate concentrations. However, no inhibition was observed at high concentration of phosphate ion, which was distinctly different in case of other Class II fumarases. In industrial process, the reaction temperatures for L-malate production are usually set between 40 and 60 °C. The recombinant SlFumC displayed maximal activity at 45 °C and remained over 85 % of original activity after 48 h incubation at 40 °C, which was more thermostable than other fumarases from Streptomyces and make it an efficient enzyme for use in the industrial production of L-malate.

Design and Synthesis of Functionally Active 5-Amino-6-Aryl Pyrrolopyrimidine Inhibitors of Hematopoietic Progenitor Kinase 1.

Immune activating agents represent a valuable class of therapeutics for the treatment of cancer. An area of active research is expanding the types of these therapeutics that are available to patients via targeting new biological mechanisms. Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of immune signaling and a target of high interest for the treatment of cancer. Herein, we present the discovery and optimization of novel amino-6-aryl pyrrolopyrimidine inhibitors of HPK1 starting from hits identified via virtual screening. Key components of this discovery effort were structure-based drug design aided by analyses of normalized B-factors and optimization of lipophilic efficiency.

Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts.

Nucleic acids were found to partition into the phenol phase during phenol extraction in the presence of guanidinium at certain concentrations under acidic conditions. The guanidinium-concentration-dependent nucleic acid partitioning patterns were analogous to those of the nucleic acid adsorption/partitioning onto silica mediated by guanidinium, which implied that phenol and silica interact with nucleic acids through similar mechanisms. A competition effect was observed in which the nucleic acids that had partitioned into the phenol phase or onto the silica solid phase could be recovered to the aqueous phases by potassium in a molecular weight-salt concentration-dependent manner (the higher molecular weight nucleic acids needed higher concentrations of potassium to be recovered, and vice versa). Methods were developed based on these findings to isolate total RNA from Escherichia coli. By controlling the concentrations of guanidinium and potassium salts used before phenol extraction or silica adsorption, we can selectively recover total RNA but not the high molecular weight genomic DNA in the aqueous phases. Genomic DNA-free total RNA obtained by our methods is suitable for RT-PCR or other purposes. The methods can also be adapted to isolate small RNAs or RNA in certain molecular weight ranges by changing the salt concentrations used.

[Clinical Application of Screening Cell Combination Method in the Prediction of Red Blood Cell Alloantibody].

OBJECTIVE: To explore the clinical application of screening cell combination method in the prediction of red blood cell alloantibody, so as to provide basis for clinical diagnosis. METHODS: From October 2018 to April 2020, 9 680 samples were screened with automatic blood group instrument, 79 patients with positive alloantibodies were identified by 4 sets of screening cells from different manufacturers (referred to as combined method). At the same time, cell panel Panocell-16 was used for comparative analysis. Meanwhile, the combined method was also used to identify the antibodies of 20 samples from National Center for Clinical Laboratories external quality assessment (EQA) in China and 12 samples from WHO EQA. RESULTS: The 79 alloantibodies included anti-Mia antibody (7 cases), anti-M antibody (13 cases), anti-Lea antibody (9 cases), anti-P1 antibody (2 cases), anti-E antibody (22 cases), anti-c + E antibody (9 cases), anti-D antibody (4 cases), anti-e antibody (2 cases), anti-C + e antibody (3 cases), anti-C antibody (3 cases), anti-H antibody (1 case), anti-Fyb antibody (1 case), anti-E + M antibody (1 case), autoantibody + anti-E (2 cases). However, 7 cases of anti-Mia antibody and 1 case of anti- Lea antibody were missed in Panocell-16 identification results. The results of antibody identification in 20 samples from National Center for Clinical Laboratories EQA in China and 12 samples from WHO EQA were 100% accurate by combination method. The identification results between combined method identification and Panocell-16 identification showed no significant difference. CONCLUSION: The combined method can identify the alloantibodies of red blood cells in Chinese population. The screening cells can be used for screening of irregular antibodies without wasting reagents at the same time.

[Expression and characterization of lipase LpsA2 from Streptomyces avermitilis].

OBJECTIVE: We expressed the lipase gene lpsA2 from Streptomyces avermitilis in Escherichia coli and characterized the enzymatic properties of LpsA2. METHODS: We extracted the genomic DNA of S. avermitilis and amplified lpsA2 gene by PCR with specific primers. We then expressed lpsA2 gene in E. coli and determined the enzymatic properties of LpsA2. We also analyzed the evolutionary relationship between LpsA2 and lipase family by using phylogenetic tree based on the alignment of amino acid sequences. RESULTS: According to the alignment of amino acid sequences, we found that LpsA2 had the active site (Ser130-Asp221-His253) which was consistent with the typical characteristics of lipases that their active centers always consisted of Ser, His and Asp, and Ser always located in the conserved five peptide structure (Gly128-His129-Ser130-Gln131-Gly132). We constructed the evolutionary tree and found that LpsA2 belonged to Subfamily I.7 of lipase Family I. Furthermore, the optimal pH and temperature of LpsA2 were pH 8.0 and 50 degrees C, respectively. The best substrate of LpsA2 was p-nitrophenol myristate. The activation energy (Ea) of LpsA2 between 10 degrees C and 50 degrees C was 6.3 kcal/mol. The enzyme activity of LpsA2 was increased to 250% or above by 1 mmol/L Co2+, Hg2+ and Zn2+, respectively. The activity was also elevated to 110.7% and 138.0% by 15% dimethylformamide and dimethyl sulfoxide, and 352.7% and 189.7% by 0.1% and 1% Span-20, respectively. CONCLUSION: The enzymatic properties of LpsA2 from S. avermitilis were characterized that may provide the fundament to the screening of bio-engineered bacteria and the industrial applications in food processing and drug synthesis.

Overexpression and biochemical characterization of soluble pyridine nucleotide transhydrogenase from Escherichia coli.

The soluble pyridine nucleotide transhydrogenase (STH) is an energy-independent flavoprotein that directly catalyzes hydride transfer between NAD(H) and NADP(H) to maintain homeostasis of these two redox cofactors. The sth gene in Escherichia coli was cloned and expressed as a fused protein (EcSTH). The purified EcSTH displayed maximal activity at 35 °C, pH 7.5. Heat-inactivation studies showed that EcSTH retains 50% activity after 5 h at 50 °C. The enzyme was stable at 4 °C for 25 days. The apparent K(m) values of EcSTH were 68.29 µM for NADPH and 133.2 µM for thio-NAD(+) . The k(cat) /K(m) ratios showed that EcSTH had a 1.25-fold preference for NADPH over thio-NAD(+) . Product inhibition studies showed that EcSTH activity was strongly inhibited by excess NADPH, but not by thio-NAD(+) . EcSTH activity was enhanced by 2 mM adenine nucleotide and inhibited by divalent metal ions: Mn(2+) , Co(2+) , Zn(2+) , Ni(2+) and Cu(2+) . However, after preincubation for 30 min, most divalent metal ions had little effect on EcSTH activity, except Zn(2+) , Ni(2+) and Cu(2+) . The enzymatic analysis could provide the important basic knowledge for EcSTH utilizations.

Enzymatic characterization of isocitrate dehydrogenase from an emerging zoonotic pathogen Streptococcus suis.

Streptococcus suis, a Gram-positive coccus, is an emerging zoonotic pathogen for both humans and pigs, but little is known about the properties of its metabolic enzymes. Isocitrate dehydrogenase (IDH) is a key regulatory enzyme in the citric acid cycle that catalyzes the oxidative decarboxylation of isocitrate yielding α-ketoglutarate and NAD(P)H. Here, we report the overexpression and enzymatic characterization of IDH from S. suis Serotype 2 Chinese highly virulent strain 05ZYH33 (SsIDH). The molecular weight of SsIDH was estimated to be 74 kDa by gel filtration chromatography, suggesting a homodimeric structure. Additionally, SsIDH was divalent cation-dependent and Mg(2+) was found to be the most effective cation. The optimal pH of SsIDH was 7.0 (Mn(2+)) and 8.5 (Mg(2+)), and the maximum activity was around 30 °C (Mn(2+)) and 50 °C (Mg(2+)), respectively. Heat inactivation studies showed that SsIDH retained 50% activity after 20 min of incubation at 49 °C. Sequence comparison revealed that SsIDH had a significantly homologous identity to bacterial homodimeric IDHs. The recombinant SsIDH displayed a 117-fold (k(cat)/K(m)) preference for NAD(+) over NADP(+) with Mg(2+), and a 80-fold greater specificity for NAD(+) than NADP(+) with Mn(2+). Therefore, SsIDH has remarkably high coenzyme preference toward NAD(+). This current work is expected to shed light on the functions of metabolic enzymes in S. suis and provide useful information for SsIDH to be considered as a possible candidate for serological diagnostics and detection of S. suis infection.

Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli.

Malic enzymes catalyze the reversible oxidative decarboxylation of L-malate using NAD(P)(+) as a cofactor. NADP-dependent malic enzyme (MaeB) from Escherichia coli MG1655 was expressed and purified as a fusion protein. The molecular weight of MaeB was about 83 kDa, as determined by SDS-PAGE. The recombinant MaeB showed a maximum activity at pH 7.8 and 46°C. MaeB activity was dependent on the presence of Mn(2+) but was strongly inhibited by Zn(2+). In order to understand the physiological roles, recombinant E. coli strains (icd (NADP)/ΔmaeB and icd (NAD)/ΔmaeB) containing NADP-dependent isocitrate dehydrogenase (IDH), or engineered NAD-dependent IDH with the deletion of the maeB gene, were constructed using homologous recombination. During growth on acetate, icd (NAD)/ΔmaeB grew poorly, having a growth rate only 60% that of the wild-type strain (icd (NADP)). Furthermore, icd (NADP)/ΔmaeB exhibited a 2-fold greater adaptability to acetate than icd (NAD)/ΔmaeB, which may be explained by more NADPH production for biosynthesis in icd (NADP)/ΔmaeB due to its NADP-dependent IDH. These results indicated that MaeB was important for NADPH production for bacterial growth on acetate. We also observed that MaeB activity was significantly enhanced (7.83-fold) in icd (NAD), which was about 3-fold higher than that in icd (NADP), when switching from glucose to acetate. The marked increase of MaeB activity was probably induced by the shortage of NADPH in icd (NAD). Evidently, MaeB contributed to the NADPH generation needed for bacterial growth on two carbon compounds.