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Alzheimer's disease is a rapidly increasing neurodegenerative disease. It is a multifactorial disease and also a global threat. Several enzymes are implicated in the disease in which Glycogen Synthase Kinase 3 beta is a key enzyme to increase the disease progression by the hyperphosphorylation of the tau protein. We have used an integrative chemoinformatics and pharmacokinetics approach for the identification of novel small molecules. We have retrieved a subset from the ZINC database (n = 5,36,709) and screened against GSK3β in four steps. From here top 298 potent compounds were selected and employed for their pharmacokinetics analysis. We had seen that 29 compounds showed the key characteristics to be a novel drug candidate therefore, all these compounds were employed for redocking studies using Autodock Vina and Autodock. This analysis revealed that four compounds were showing good binding affinity. All these four compounds were employed for MDS analysis of 100 ns From here using a bunch of MD analyses we have found that out of four compounds GSK3β-ZINC21011059 and GSK3β-ZINC21011066 act as a stable protein-ligand complex. Therefore we proposed ZINC21011059 and ZINC21011066 can serve as a novel compounds against GSK3β and predicted scaffold can be used for further optimization towards the improvement of isoform selectivity, and warranting further investigations towards their in vitro and in vivo validation of the bioactivity. Image 1 • The subset of the compounds (n = 5,36,709) was screened against GSK3β in four steps and followed by redocking. • The 298 compounds were evaluated using pharmacokinetic assay and selected 29 compounds were evaluated by redocking approach. • We have found that ZINC21011059 and ZINC21011066 showed the good binding affinity from the MDS study. • These both compounds can act as a potent inhibitor against the GSK3β. [ABSTRACT FROM AUTHOR]

Ascorbate has been demonstrated to interfere with the growth of Mycobacterium tuberculosis . It scavenges oxygen in the culture medium to induce dormancy of M. tuberculosis . It kills the mycobacteria by generating reactive oxygen intermediates via iron mediated Fenton reactions. In this study, we observed that ascorbate can inhibit M. tuberculosis isocitrate lyase (MtbICL) with an IC 50 of 2.15 mΜ. MtbICL is an essential enzyme for the survival of M. tuberculosis under dormancy. We studied the effect of ascorbate on the growth of M. tuberculosis H37Rv metabolizing through citric acid cycle or glyoxylate cycle with glucose or acetate respectively as the sole carbon source. It was observed that 4 mM ascorbate inhibited ∼89% of the growth in glucose medium, which was confirmed to be mediated by Fenton reaction, as the inhibition was significantly lesser (61%) under low iron condition. On the other hand, in acetate medium, ∼97% of the growth was inhibited and the inhibition was uninfluenced by the iron levels. 3-nitropropionate, a known inhibitor of MtbICL, was seen to cause significantly higher inhibition in the acetate medium than in the glucose medium; however it was indifferent to iron levels in either medium. Molecular docking and dynamic simulation studies confirmed stable binding of ascorbate to MtbICL leading to its inhibition. These observations suggest an additional pathway for ascorbate induced inhibition of M. tuberculosis through inhibition of glyoxylate cycle. Since human immune cells can accumulate ascorbate in millimolar concentrations, the in vitro activity range (1–4 mM) of ascorbate against M. tuberculosis could be extrapolated in vivo . Our result supports the possible benefits of adding high vitamin C diet in TB-treated patients. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a crucial enzyme of the glyoxylate cycle and is a validated anti-tuberculosis drug target. Structurally distant, non-active site mutation (H46A) in MtbICL has been found to cause loss of enzyme activity. The aim of the present work was to explore the structural alterations induced by H46A mutation that caused the loss of enzyme activity. The structural and dynamic consequences of H46A mutation were studied using multiple computational methods such as docking, molecular dynamics simulation and residue interaction network analysis (RIN). Principal component analysis and cross correlation analysis revealed the difference in conformational flexibility and collective modes of motions between the wild-type and mutant enzyme, particularly in the active site region. RIN analysis revealed that the active site geometry was disturbed in the mutant enzyme. Thus, the dynamic perturbation of the active site led to enzyme transition from its active form to inactive form upon mutation. The computational analyses elucidated the mutant-specific conformational alterations, differential dominant motions, and anomalous residue level interactions that contributed to the abrogated function of mutant MtbICL. An understanding of interactions of mutant enzymes may help in modifying the existing drugs and designing improved drugs for successful control of tuberculosis. [ABSTRACT FROM AUTHOR]

Peroxides are one of the most important radicals that cause oxidative stress. Certain Glutathione S-transferases (GSTs) have been reported to show peroxidase activity. We report a novel peroxidase activity of Synechocystis GST- sll1545. The recombinant protein was purified to homogeneity and characterized. Low K m (0.109 μM) and high V max (0.663 μmol min −1 ) values suggest a high preference of sll1545 for cumenehydroperoxide. Disc inhibition assay confirmed the ability of the enzyme to protect cells against peroxide-induced damage. sll1545 has very low sequence and structural similarity with theta and alpha class GSTs that exhibit glutathione-dependent peroxidase activity. Recent data from our laboratory shows that sll1545 is also strongly active against dichloroacetate (DCA), which is a characteristic of zeta class GST. Interestingly, sll1545 shows less than 20% sequence identity with zeta class GST. Molecular dynamic simulation results show that sll1545 was much more structurally different from alpha/theta classes. Our results suggest that sll1545 shows structural variation from zeta, theta/alpha classes of GSTs but have related enzymatic activity. Phylogenetic analysis reveal that sll1545 is evolutionally very distinct from the known GSTs. Overall, the data suggest that Synechocystis sll1545 does not belong to any known GST class and represent a novel GST class, which we have named rho. [ABSTRACT FROM AUTHOR]

Abstract Peptidoglycan (PG) is the main constituent of the bacterial cell wall. The enzyme UDP‑ N ‑acetylglucosamine enolpyruvyl transferase (MurA) catalyzes the transfer of enolpyruvate from phosphoenolpyruvate to uridinediphospho‑ N ‑acetylglucosamine, which is the first committed step of PG biosynthesis. In this study, we have systematically examined the urea-induced unfolding of Acinetobacter baumannii MurA (AbMurA) using various optical spectroscopic techniques and molecular dynamics (MD) simulations. The urea-induced unfolding of AbMurA was a three-state process, where a metastable intermediate conformation state is populated between 3.0 and 4.0 M. Above 6.0 M urea, AbMurA gets completely unfolded. The transition from the native structure to the partially unfolded metastable state involves ~30% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate-to-unfolded state transition was characterized by a large increase in the radius of gyration. MD trajectories simulated in different unfolding conditions suggest that urea destabilizes AbMurA structure weakening hydrophobic interactions and the hydrogen bond network. We observed a clear correlation between both in vitro and in silico studies. To our knowledge, this is also the first report on unfolding/stability analysis of any MurA enzyme. Highlights • Urea-induced unfolding of AbMurA were examined using spectroscopic techniques and MD simulations. • Unfolding of AbMurA was a three-state process, with the presence of a metastable intermediate conformation state. • Transition from the native-to-metastable state involves ~30% loss of native contacts but little change in the radius of gyration. • Intermediate-to-unfolded state transition was characterized by a large increase in the radius of gyration. • Urea destabilizes AbMurA structure by weakening hydrophobic interactions and the hydrogen bond network. [ABSTRACT FROM AUTHOR]

Abstract Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a major component of the yeast pre-mRNA 3′-end processing factor, the cleavage factor IA complex, and is involved in cleavage and polyadenylation of mRNA in the nucleus. Rna14 is also essential for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe. In the present study, we report that a non-homologous mutation, A394E that is present in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. This mutation was shown to disrupt chromosome segregation and 3′-end maturation, and also affects the pre-mRNA splicing in vivo at non-permissive temperatures. We observed that a significant part of Rna14 is intrinsically disordered, that includes the N- and C-terminal of Rna14, as well as the central region containing the HAT repeats and the mutation within amino acid residues 372–435. These regions are crucial for the function of Rna14 as they are involved in the interaction of Rna14 with other proteins. Highlights • Rna14 is essential for the maintenance of genomic integrity in fission yeast S. pombe. • Here, we report that a point mutation, A394E in the central IDR of Rna14 leads to chromosomal instability in fission yeast. • This mutation disrupts chromosome segregation, 3′-end maturation, and the pre-mRNA splicing. • Significant part of Rna14 was intrinsically disordered, that includes the regions that are crucial for the interaction of Rna14 with other proteins. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • A computational approach to identify natural inhibitors of Xanthine oxidoreductase from Millets. • Comparative docking studies of identified millet derived compound(s) with available drugs were performed. • Based on RMSD, RMSF, Radius of gyration, PCA, Gibbs free energy and binding free energy values of the simulated protein-ligand complexes, it was concluded that the selected millet derived compounds displayed identical and even better activity than the reference drugs i.e. Febuxostat and Allopurinol. • It was analysed that Luteolin possesses more stability with good ADMET properties. Therefore, it is capable to inhibit the overexpression of HsXOR’s by regulating uric acid pathway. Abstract Xanthine oxidoreductase plays an important role in formation of uric acid and its regulation during purine catabolism. Uncontrolled expression of this enzyme is responsible for overproduction and deposition of uric acid in blood that is potentially injurious because it can breakdown DNA and protein molecules, triggering many diseases. Human Xanthine oxidoreductase (HsXOR) is considered to be a pharmacological target for the treatment of hyperuricemia. Many of the HsXOR-inhibitor drugs such as Febuxostat and Allopurinol are known to have significant adverse effects. Therefore, there is an urgent need to develop new HsXOR-inhibitor drugs with less or no toxicity for the long-term treatment or prevention of hyperuricemia-related diseases. Many nutritious and medical functions have been reported in millets. Present work deals with identification of millet derived compounds in terms of their interaction with target, HsXOR through molecular docking and dynamic simulation studies. Of thirty two chosen compounds, Luteolin and Quercitin showed more binding affinity with HsXOR than reference drugs, Febuxostat and Allopurinol. Molecular dynamics simulations (20 ns long) revealed that Luteolin-protein complex was energetically more stable than Quercitin-protein complex. The millet derived compounds i.e. Luteolin and Quercitin showed binding energy −9.7 kcal/mol whereas the known drugs i.e. Febuxostat and Allopurinol showed binding energy −8.0 kcal/mol and −5.5 kcal/mol respectively. Based on the study, Luteolin possess high potential to be considered for trial as an inhibitor of HsXOR as it may regulate the pathway by inhibiting HsXOR. Further investigations are proposed to consider Luteolin for developing future drugs from millets and other natural sources. [ABSTRACT FROM AUTHOR]

The thiol-disulfide redox metabolism in platyhelminth parasites depends entirely on a single selenocysteine (Sec) containing flavoenzyme, thioredoxin glutathione reductase (TGR) that links the classical thioredoxin (Trx) and glutathione (GSH) systems. In the present study, we investigated the catalytic and structural properties of different variants of Fasciola gigantica TGR to understand the role of Sec. The recombinant full-length Sec containing TGR (FgTGRsec), TGR without Sec (FgTGR) and TGRsec without the N-terminal glutaredoxin (Grx) domain (∆NTD-FgTGRsec) were purified to homogeneity. Biochemical studies revealed that Sec597 is responsible for higher thioredoxin reductase (TrxR) and glutathione reductase (GR) activity of FgTGRsec. The N-terminal Grx domain was found to positively regulate the DTNB-based TrxR activity of FgTGRsec. The FgTGRsec was highly sensitive to inhibition by auranofin (AF). The structure of FgTGR was modeled, and the inhibitor AF was docked, and binding sites were identified. Unfolding studies suggest that all three proteins are highly cooperative molecules since during GdnHCl-induced denaturation, a monophasic unfolding of the proteins without stabilization of any intermediate is observed. The C m for GdnHCl induced unfolding of FgTGR was higher than FgTGRsec and ∆NTD-FgTGRsec suggesting that FgTGR without Sec was more stable in solution than the other protein variants. The free energy of stabilization for the proteins was also determined. To our knowledge, this is also the first report on unfolding and stability analysis of any TGR. [ABSTRACT FROM AUTHOR]

Peptidoglycan (PG) is the key component of the bacterial cell wall. The enzyme UDP- N -Acetylglucosamine Enolpyruvyl Transferase (MurA) catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridinediphospho- N -acetylglucosamine (UNAG), which is the first committed step of PG biosynthesis. Here, we present the biochemical and structural features of the MurA enzyme of the opportunistic pathogen Acinetobacter baumannii (AbMurA). The recombinant AbMurA exists as a monomer in solution and shows optimal activity at pH 7.5 and 37 °C. The K m for UDP- N -acetylglucosamine was 1.062 ± 0.09 mM and for PEP was 1.806 ± 0.23 mM. The relative enzymatic activity was inhibited ∼3 fold in the presence of 50 mM fosfomycin (FFQ). Superimposition of the AbMurA model with E. coli demonstrated key structural similarity in the FFQ-binding site. AbMurA also has a surface loop that contains the active site Cys116 that interact with FFQ. Sequence analysis indicates the presence of the five conserved amino acids, i.e., K22, C116, D306, D370 and L371, required for the functional activity like other MurA enzymes from different bacteria. MurA enzymes are indispensable for cell integrity and their lack of counterparts in eukaryotes suggests them to be a promising drug target. [ABSTRACT FROM AUTHOR]

• A homolog of Caenorhabditis elegans sterol-binding protein-1 was identified in Meloidogyne incognita. • Mi-sbp-1 is a transcriptional regulator of several lipogenesis pathway genes. • In-vitro and host-induced RNA interference silencing of Mi-sbp-1 reduced nematode parasitism. • Mi-sbp-1 can be used as a target for the management of M. incognita. • This approach can be extended to manage other parasitic nematodes. Meloidogyne incognita is a polyphagous plant-parasitic nematode that causes considerable yield loss in agricultural and horticultural crops. The management options available for M. incognita are extremely limited. Here we identified and characterised a M. incognita homolog of Caenorhabditis elegans sterol-binding protein (Mi-SBP-1), a transcriptional regulator of several lipogenesis pathway genes, and used RNA interference-mediated gene silencing to establish its utility as a target for the management of M. incognita. Mi-sbp-1 is predicted to be a helix-loop-helix domain containing DNA binding transcription factor, and is present in the M. incognita genome in three copies. The RNA-Seq analysis of Mi-sbp-1 silenced second stage juveniles confirmed the key role of this gene in lipogenesis regulation in M. incognita. In vitro and host-induced gene silencing of Mi-sbp-1 in M. incognita second stage juveniles resulted in loss of nematodes' ability to utilise the stored fat reserves, slower nematode development, and reduced parasitism on adzuki bean and tobacco plants. The multiplication factor for the Mi-sbp-1 silenced nematodes on adzuki bean plants was reduced by 51% compared with the control nematodes in which Mi-sbp-1 was not silenced. Transgenic expression of the double-stranded RNA construct of the Mi-sbp-1 gene in tobacco plants caused 40–45% reduction in M. incognita multiplication, 30–43.8% reduction in the number of egg masses, and 33–54% reduction in the number of eggs per egg mass compared with the wild type control plants. Our results confirm that Mi-sbp-1 is a key regulator of lipogenesis in M. incognita and suggest that it can be used as an effective target for its management. The findings of this study can be extended to develop methods to manage other economically important parasitic nematodes. [ABSTRACT FROM AUTHOR]

Abstract: A novel chemo-enzymatic synthesis of (S)-rivastigmine using ketoreductases with NADH/NADPH as the proton donor has been demonstrated. An exclusive enzymatic process has been developed by exploring the possible ketoreductases by screening to identify enzymes useful for the preparation of the (S)-isomer intermediate, and scaling up of the enzymatic process for the production of an adequate, enantiomerically pure precursor of rivastigmine and for the total synthesis of (S)-rivastigmine. [Copyright &y& Elsevier]

• Improved draft genome assembly for Meloidogyne graminicola IARI strain is presented. • Long-read sequencing resulted in 36.86 Mb genome assembly with 514 contigs. • 14,062 protein-coding gene models were predicted. • 5 CAZymes were found in M. graminicola but not in other root-knot nematodes. • This assembly would facilitate better comparative and functional genomics. The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola. [ABSTRACT FROM AUTHOR]

Zirconium based alloys are proved to be a good material for hydrogen storage as well as a vacuum pump. A non evaporable getter pump based on St 172 was tested for deuterium storage capacity in a sealed off vacuum device. The vacuum in the range of ultra high vacuum was maintained by the getter pump by gettering. Initial vacuum was created by a turbo molecular pumping system. After activation of the getter, test chamber was charged at 1 bar and 3 bar deuterium pressure for 24 h in two different experimental campaigns. After charging with deuterium, the chamber was pumped to ultimate vacuum and isolated from the TMP. The partial pressure of deuterium for different temperature of the getter was measured in sealed condition. Higher charging pressure improves the partial pressure of deuterium during desorption cycle. The experimental details and the results are presented in this article. • St 172 NEG was tested for use as deuterium source in sealed off vacuum device. • Higher charging of deuterium is effective to get higher operational pressure. • Higher charging helps for low temperature operation for specific deuterium pressure. [ABSTRACT FROM AUTHOR]