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The design, synthesis and biological evaluation of novel thiamin diphosphate analog inhibitors against the pyruvate dehydrogenase multienzyme complex E1 from Escherichia coli.
Org. Biomol. Chem.
PUBLISHED: 10-01-2014
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Pyruvate dehydrogenase multienzyme complex E1 (PDHc E1) is a potential target enzyme when looking for inhibitors to combat microbial disease. In this study, we designed and synthesized a series of novel thiamin diphosphate (ThDP) analogs with triazole ring and oxime ether moieties as potential inhibitors of PDHc E1. Their inhibitory activities against PDHc E1 were examined both in vitro and in vivo. Most of the tested compounds exhibited moderate inhibitory activities against PDHc E1 (IC50 = 6.1-75.5 ?M). The potent inhibitors , and , had strong inhibitory activities with IC50 values of 6.7, 6.9 and 6.1 ?M against PDHc E1 in vitro and with inhibition rates of 35%, 50% and 33% at 100 ?g mL(-1) against Gibberella zeae in vivo, respectively. The binding mode of to PDHc E1 was analyzed by a molecular docking method. Furthermore, the possible interactions of the important residues of PDHc E1 with compound were examined by site-directed mutagenesis, enzymatic assays and spectral fluorescence studies. The theoretical and experimental results are in good agreement and suggest that compound could be used as a lead compound for further optimization, and may have potential as a new microbicide.
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Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory.
J Comput Chem
PUBLISHED: 07-10-2014
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Within the framework of the Förster theory, the electronic excitation energy transfer pathways in the cyanobacteria allophycocyanin (APC) trimer and hexamer were studied. The associated physical quantities (i.e., excitation energy, oscillator strength, and transition dipole moments) of the phycocyanobilins (PCBs) located in APC were calculated at time-dependent density functional theory (TDDFT) level of theory. To estimate the influence of protein environment on the preceding calculated physical quantities, the long-range interactions were approximately considered with the polarizable continuum model at the TDDFT level of theory, and the short-range interaction caused by surrounding aspartate residue of PCBs were taken into account as well. The shortest energy transfer time calculated in the framework of the Förster model at TDDFT/B3LYP/6-31+G* level of theory are about 0.10 ps in the APC trimer and about 170 ps in the APC monomer, which are in qualitative agreement with the experimental finding that a very fast lifetime of 0.43-0.44 ps in APC trimers, whereas its monomers lacked any corresponding lifetime. These results suggest that the lifetime of 0.43-0.44 ps in the APC trimers determined by Sharkov et al. was most likely attributed to the energy transfer of ?(1) -84 ? ?(3) -84 (0.23 ps), ?(1) -84 ? ?(2) -84 (0.11 ps) or ?(2) -84 ? ?(3) -84 (0.10 ps). So far, no experimental or theoretical energy transfer rates between two APC trimmers were reported, our calculations predict that the predominate energy transfer pathway between APC trimers is likely to occur from ?(3) -84 in one trimer to ?(5) -84 in an adjacent trimer with a rate of 32.51 ps. © 2014 Wiley Periodicals, Inc.
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Pharmacophore-based virtual screening and experimental validation of novel inhibitors against cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase.
J Chem Inf Model
PUBLISHED: 02-21-2014
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Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening of novel inhibitors that can combat harmful algal blooms. In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from the SPECs database were selected by using a pharmacophore-based virtual screening strategy. Most of the compounds tested exhibited moderate inhibitory activities (IC50 = 20.7-176.9 ?M) against cy-FBP/SBPase. Compound 2 and its analogues 10 and 11 exhibited strong inhibitory activities, with IC50 values of 20.7, 13.4, and 19.0 ?M against cy-FBP/SBPase in vitro and EC50 values of 12.3, 10.9, and 2.9 ppm against cyanobacteria Synechocystis PCC6803 in vivo, respectively. The compound 10 was selected in order to perform a refined docking study to investigate the rational binding mode of inhibitors with cy-FBP/SBPase. Furthermore, possible interactions of the residues with inhibitors were examined by site-directed mutagenesis, enzymatic assays, and fluorescence spectral analyses. The results provide insight into the binding mode between the inhibitors and the substrate binding pocket. The observed theoretical and experimental results are in concert, indicating that the modeling strategies and screening methods employed are appropriate to search for novel lead compounds having both structural diversity and high inhibitory activity against cy-FBP/SBPase.
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Overexpression of CyclinA2 ameliorates hypoxia-impaired proliferation of cardiomyocytes.
Exp Ther Med
PUBLISHED: 02-16-2014
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Hypoxia is a primary mediator for cell survival, and has been reported to inhibit cardiomyocyte proliferation in fetal and neonatal hearts. CyclinA2 is a key regulator of cell proliferation. Whether CyclinA2 affects cardiomyocyte proliferation in hypoxic conditions remains unexamined. This study was designed to investigate the roles of CyclinA2 expression on hypoxia-impaired cardiomyocyte proliferation. Cardiomyocytes were isolated from neonatal rats and randomly separated into six groups: Control, hypoxia, enhanced green fluorescent protein (EGFP)-Adv, EGFP-Ccna2, EGFP-Adv + hypoxia and EGFP-Ccna2 + hypoxia. The cells in the control group were cultured in a general cell incubator; the cells in the hypoxia group were placed in a hypoxic chamber for 12 h; the cells in the EGFP-Adv and EGFP-Ccna2 groups were separately transfected with EGFP-adenovirus capsids or EGFP-adenovirus capsids with CyclinA2 cDNA for 18 h, and then placed in a general incubator for an additional 12 h; the cells in the EGFP-Adv + hypoxia and EGFP-Ccna2 + hypoxia groups were separately transfected with EGFP-adenovirus capsids or EGFP-adenovirus capsids with CyclinA2 cDNA for 18 h, and then placed in a hypoxia chamber for an additional 12 h. CyclinA2 expression was measured using immunochemical staining and western blot analysis, and cardiomyocyte proliferation was measured using the cell counting kit 8. GFP fluorescence indicated a high transfection efficiency (>80%), and immunochemical staining showed that CyclinA2 was mainly distributed in the nucleus. CyclinA2 expression was downregulated following exposure to hypoxia for 12 h. Cardiomyocyte proliferation was also significantly decreased following exposure to hypoxia for 12 h. However, compared with the EGFP-Adv group, CyclinA2 expression and cardiomyocyte proliferation was markedly increased in the EGFP-Ccna2 group. Furthermore, compared with the EGFP-Adv + hypoxia group, CyclinA2 expression and cell proliferation were markedly increased in the EGFP-Ccna2 + hypoxia group. These findings indicate that CyclinA2 upregulation improves cardiomyocyte proliferation in hypoxic conditions.
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Structural and biochemical characterization of fructose-1,6/sedoheptulose-1,7-bisphosphatase from the cyanobacterium Synechocystis strain 6803.
FEBS J.
PUBLISHED: 10-22-2013
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Cyanobacterial fructose-1,6/sedoheptulose-1,7-bisphosphatase (cy-FBP/SBPase) plays a vital role in gluconeogenesis and in the photosynthetic carbon reduction pathway, and is thus a potential enzymatic target for inhibition of harmful cyanobacterial blooms. Here, we describe the crystal structure of cy-FBP/SBPase in complex with AMP and fructose-1,6-bisphosphate (FBP). The allosteric inhibitor AMP and the substrate FBP exhibit an unusual binding mode when in complex with cy-FBP/SBPase. Binding mode analysis suggested that AMP bound to the allosteric sites near the interface across the up/down subunit pairs C1C4 and C2C3 in the center of the tetramer, while FBP binds opposite to the interface between the horizontal subunit pairs C1C2 or C3C4. We identified a series of residues important for FBP and AMP binding, and suggest formation of a disulfide linkage between Cys75 and Cys99. Further analysis indicates that cy-FBP/SBPase may be regulated through ligand binding and alteration of the structure of the enzyme complex. The interactions between ligands and cy-FBP/SBPase are different from those of ligand-bound structures of other FBPase family members, and thus provide new insight into the molecular mechanisms of structure and catalysis of cy-FBP/SBPase. Our studies provide insight into the evolution of this enzyme family, and may help in the design of inhibitors aimed at preventing toxic cyanobacterial blooms.
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Structure-based design and synthesis of novel dual-target inhibitors against cyanobacterial fructose-1,6-bisphosphate aldolase and fructose-1,6-bisphosphatase.
J. Agric. Food Chem.
PUBLISHED: 07-26-2013
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Cyanobacteria class II fructose-1,6-bisphoshate aldolase (Cy-FBA-II) and cyanobacteria fructose-1,6-bisphosphatase (Cy-FBPase) are two neighboring key regulatory enzymes in the Calvin cycle of the cyanobacteria photosynthesis system. Each of them might be taken as a potential target for designing novel inhibitors to chemically control harmful algal blooms (HABs). In the present paper, a series of novel inhibitors were rationally designed, synthesized, and optimized based upon the structural and interactional information of both Cy-FBA-II and Cy-FBPase, and their inhibitory activities were examined in vitro and in vivo. The experimental results showed that compounds L19e-L19g exhibited moderate inhibitory activities (IC50 = 28.1-103.2 ?M) against both Cy-FBA-II and Cy-FBPase; compounds L19a-L19d, L19h, L20a-L20d exhibited high Cy-FBA-II inhibitory activities (IC50 = 2.3-16.9 ?M) and moderate Cy-FBPase inhibitory activities (IC50 = 31.5-141.2 ?M); however, compounds L20e-L20h could potently inhibit both Cy-FBA-II and Cy-FBPase with IC50 values less than 30 ?M, which demonstrated more or less dual-target inhibitors feature. Moreover, most of them exhibited potent algicide activity (EC50 = 0.8-22.3 ppm) against cyanobacteria Synechocystis sp. PCC 6803.
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Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory.
J Comput Chem
PUBLISHED: 01-08-2013
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In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C-phycocyanin (C-PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C-PC were examined by model chemistry in gas phase at time-dependent density functional theory (TDDFT), configuration interaction-singles (CIS), and Zerners intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long-range pigment-protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short-range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long- and short-range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6-31+G* level were in good agreement with the experimental results of C-PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C-PC monomer is predominant from ?-155 to ?-84 (1/K = 13.4 ps), however, from ?-84 of one monomer to ?-84 (1/K = 0.3-0.4 ps) in a neighbor monomer in C-PC trimer. In C-PC hexamer, an additional energy flow was predicted to be from ?-155 (or ?-84) in top trimer to adjacent ?-155 (or ?-84) (1/K = 0.5-2.7 ps) in bottom trimer.
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Study on the interaction between cyanobacteria FBP/SBPase and metal ions.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 10-28-2011
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Fructose-1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) is a potential important target enzyme for finding inhibitors to solve harmful algal bloom. In this paper, the interactions between FBP/SBPase and metal ions were studied by enzyme activity analysis, fluorescence and molecular modeling method. The enzyme activity analysis showed that FBP/SBPase can be activated by Mg2+ or Mn2+ but cannot be activated by Ca2+ or Zn2+. Spectroscopic analysis of emission quenching showed that quenching mechanism of FBP/SBPase with Mg2+ or Mn2+ was static quenching mechanism while that of Ca2+ or Zn2+ was dynamic quenching process. Hydrogen bonds and van der Waals interaction might be the predominant intermolecular forces in stabilizing FBP/SBPase-Mg2+ while hydrophobic forces were the predominant intermolecular forces in stabilizing FBP/SBPase-Mn2+. Microenvironment and conformation of FBP/SBPase were changed in binding reaction. The effect of metal ions and important amino acid residues on FBP/SBPase-metal ion complex was also discussed by molecular modeling study.
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Structure-based rational design of novel hit compounds for pyruvate dehydrogenase multienzyme complex E1 components from Escherichia coli.
Bioorg. Med. Chem.
PUBLISHED: 09-15-2011
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Pyruvate dehydrogenase multienzyme complex (PDHc) E1 component plays a pivotal role in cellular metabolism to convert the product of glycolysis (pyruvate) to acetyl-CoA, and has been reported as a potential target for anti-microbial and herbicide. In present study, based on the thiamin diphosphate (ThDP) site, four novel hit compounds with high inhibitory activity against the PDHc-E1 from Escherichia coli were firstly designed by using structure-based molecular docking methods. As expected, among four compounds, the compound 3a is the best inhibitor by far, with IC(50) value of 6.88 ?M against PDHc-E1 from E. coli. To elucidate the interaction mechanism between the active site of PDHc-E1 and its inhibitor, the docking-based molecular dynamics simulation (MD) and MD-based ab initio fragment molecular orbital (FMO) calculations were also further performed. The positive results indicated that all modeling strategies presented in the current study most like to be an encouraging way in design of novel lead compounds with structural diversity for PDHc-E1 in the future.
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Rapid catalytic microwave method to damage Microcystis aeruginosa with FeCl3-loaded active carbon.
Environ. Sci. Technol.
PUBLISHED: 04-22-2011
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In recent years, effective methods for cyanobacterial blooms treatment have been an important issue. In this study, we demonstrated a rapid catalytic microwave method to deal with Microcystis aeruginosa with FeCl(3)-loaded active carbon. Microcystis aeruginosa damage process was monitored by measuring optical density, chlorophyll-a content, superoxide dismutase activity, l-glutathione content, and turbidity of the treated Microcystis aeruginosa suspension. It was found that this method could quickly and efficiently induce the degradation of Microcystis aeruginosa. On the basis of control experiments and characterization results, we attributed the excellent catalytic performance to the synergy effect between hole-doping of the catalyst and hot spot of microwave irradiation. This work provides a fast and green treatment method for cyanobacterial blooms.
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Specific inhibitions of annonaceous acetogenins on class II 3-hydroxy-3-methylglutaryl coenzyme A reductase from Streptococcus pneumoniae.
Bioorg. Med. Chem.
PUBLISHED: 02-01-2011
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3-Hydroxy-3-methylglutaryl coenzyme A reductase (class II HMGR) could serve as a potential target to discover drugs fighting against the invasive diseases originated from Streptococcus pneumoniae, one of the major causes of bacterial disease in human. However, no strongly effective inhibitors of class II HMGR have been found so far. In the present study, for the first time, four annonaceous acetogenins (ACGs) were explored for the inhibition on S. pneumoniae HMGR. The results showed that the ACGs had higher inhibitory activities against S. pneumoniae HMGR with K(i) values in the range of 6.45-20.49 ?M than the statin drug lovastatin (K(i)=116.25 ?M), a classical inhibitor of class I HMGR. Then, three-dimensional modeling and docking simulations analyzed the possible binding mode of ACGs to S. pneumoniae HMGR and suggested a kind of novel structural and binding mode for designing promising inhibitor candidates of the targeted enzyme S. pneumoniae II HMGR.
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Purification, crystallization and preliminary X-ray analysis of 3-hydroxy-3-methylglutaryl-coenzyme A reductase of Streptococcus pneumoniae.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
PUBLISHED: 06-29-2010
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Class II 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductases are potential targets for novel antibiotic development. In order to obtain a precise structural model for use in virtual screening and inhibitor design, HMG-CoA reductase of Streptococcus pneumoniae was cloned, overexpressed and purified to homogeneity using Ni-NTA affinity chromatography. Crystals were obtained using the hanging-drop vapour-diffusion method. A complete data set was collected from a single frozen crystal on a home X-ray source. The crystal diffracted to 2.3?Å resolution and belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 773.4836, b = 90.3055, c = 160.5592?Å, ? = ? = ? = 90°. Assuming the presence of two molecules in the asymmetric unit, the solvent content was estimated to be 54.1% (V(M) = 2.68?Å(3)?Da(-1)).
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New cobalt-mediated radical polymerization (CMRP) of methyl methacrylate initiated by two single-component dinuclear ?-diketone cobalt (II) catalysts.
PLoS ONE
PUBLISHED: 02-18-2010
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Two dinuclear cobalt complexes based on bis-diketonate ligands (ligand 1: 3,3-(1,3-phenylene)bis(1-phenylpropane-1,3-dione); ligand 2: 3,3-(1,4-phenylene)bis(1-phenylpropane-1,3-dione)) were successfully synthesized. The two neutral catalysts all showed satisfactory activities in the cobalt-mediated radical polymerization (CMRP) of methyl methacrylate (MMA) with the common initiator of azodiisobutyronitrile (AIBN). The resulting polymerizations have all of the characteristics of a living polymerization and displayed linear semilogarithmic kinetic plots, a linear correlation between the number-average molecular weight and the monomer conversion, and low polydispersities. Mono- or dicomponent low polydispersity polymers could be obtained by using the two dinuclear catalysts under proper reaction conditions. All these improvements facilitate the implementation of the acrylate CMRP and open the door to the scale-up of the syntheses and applications of the multicomponent low polydispersity polymers.
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Structure-based rational screening of novel hit compounds with structural diversity for cytochrome P450 sterol 14alpha-demethylase from Penicillium digitatum.
J Chem Inf Model
PUBLISHED: 01-22-2010
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Cytochrome P450 sterol 14alpha-demethylases (CYP51s) are essential enzymes in sterol biosynthesis and well-known as the target of antifungal drugs. All fungal CYP51s are integral membrane proteins, making structural and biophysical characterization more challenging. The X-ray crystallographic structure of CYP51 isolated from Mycobacterium tuberculosis (MT-CYP51) is the unique reported one hitherto. In the present study, a homology modeling three-dimensional structure of CYP51 from Penicillium digitatum (PD-CYP51) was generated by CPHmodels, in which the accuracy of sequence alignment could be improved by taking into account further structural conservation information, using MT-CYP51 as the template. Interaction mechanism between the active site of PD-CYP51 and its inhibitors were further investigated by molecular dynamics simulating and molecular docking. With the effective docking process and interaction analysis information, structure-based virtual screening was performed to pick out the thirty new potential inhibiting compounds with structural diversity by using a new virtual screening strategy including Flex-Pharm/PMF/GOLD//FlexX/PMF/GOLD molecular docking procedures, and finally, seven new hit compounds out of SPECs database with potent inhibitory ability were validated by bioaffinity assays at enzyme level and on P. digitatum in vitro. The positive results indicated that all modeling strategies and screening processes presented in the current study most like to be an encouraging way in search of novel lead compounds with structural diversity for the specifically individual fungal CYP51s of both plants and human pathogens in the future.
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Understanding the spectroscopic properties of the photosynthetic reaction center of Rhodobacter sphaeroides by a combined theoretical study of absorption and circular dichroism spectra.
J Phys Chem B
PUBLISHED: 07-04-2009
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In the present study, we calculate eight low-lying (1.3-1.7 eV energy region) electronic excited states in well accordance with the absorption and CD spectroscopic properties of PSRC from Rb. shpaeroides by using time-dependent density functional theory (TDDFT). Our present calculations demonstrate that, only when the interactions among the prosthetic groups have been taken into account, a set of satisfactory assignments for both absorption and CD spectra of PSRC from Rb. sphaeroides can be achieved simultaneously.
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Bis(3-nitro-anilinium) sulfate.
Acta Crystallogr Sect E Struct Rep Online
PUBLISHED: 02-14-2009
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In the title salt, 2C(6)H(7)N(2)O(2) (+)·SO(4) (2-), all the non-H atoms of both cations and the S atom and two O atoms of the anion lie on a crystallographic mirror plane. In the crystal structure, N-H?O and C-H?O hydrogen bonds help to establish the packing.
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Expression of a novel OSPGYRP (rice proline-, glycine- and tyrosine-rich protein) gene, which is involved in vesicle trafficking, enhanced cold tolerance in E. coli.
Biotechnol. Lett.
PUBLISHED: 01-22-2009
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A novel OSPGYRP gene encoding a rice proline-, glycine- and tyrosine-rich protein was isolated from cold-stress treated rice seedlings using suppression subtractive hybridization. Both amino acid sequence analysis and subcellular localization confirm that OsPGYRP is a novel protein involved in vesicle trafficking. The expression of the OSPGYRP gene was induced by cold, salt, and osmotic stress. In addition, expression of the OSPGYRP gene in E. coli increased the resistance to cold stress. These results show that OsPGYRP is a novel protein involved in vesicle trafficking and plays an important role in plant adaptation to stress.
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Structure-based design and screen of novel inhibitors for class II 3-hydroxy-3-methylglutaryl coenzyme A reductase from Streptococcus pneumoniae.
J Chem Inf Model
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3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a primary target in the current clinical treatment of hypercholesterolemia with specific inhibitors of "statin" family. Statins are excellent inhibitors of the class I (human) enzyme but relatively poor inhibitors of the class II enzyme, which are well-known as a potential target to discover drugs fighting against the invasive diseases originated from S. pneumoniae . However, no significantly effective inhibitors of class II HMGR have been reported so far. In the present study, the reasonable three-dimensional (3D) structure of class II HMGR from S. pneumoniae (SP-HMGR-II) was built by Swissmodel. On the basis of the modeling 3D structure in "close" flap domain form, several novel potential hit compounds out of SPECs database were picked out by using structure-based screening strategy. Especially the compounds 4, 3, and 11 exhibit highly inhibitory activities, with IC50 values of 11.5, 18.5, and 18.1 ?M, respectively. Furthermore, the hit compounds were chosen as probe molecules, and their probable interactions with the corresponding individual residues have been examined by jointly using the molecular docking, site-directed mutagenesis, enzymatic assays, and fluorescence spectra, to provide an insight into a new special binding-model located between the HMG-CoA and NADPH pockets. The good agreement between theoretical and experimental results indicate that the modeling strategies and screening processes in the present study are very likely to be a promising way to search novel lead compounds with both structural diversity and high inhibitory activity against SP-HMGR-II in the future.
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Design, synthesis and biological evaluation of novel 2-methylpyrimidine-4-ylamine derivatives as inhibitors of Escherichia coli pyruvate dehydrogenase complex E1.
Bioorg. Med. Chem.
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As potential inhibitors of Escherichia coli pyruvate dehydrogenase complex E1 (PDHc E1), a series of novel 2-methylpyrimidine-4-ylamine derivatives were designed based on the structure of the active site of PDHc E1 and synthesized using click chemistry. Their inhibitory activity in vitro against PDHc E1 and fungicidal activity were examined. Some of these compounds such as 3g, 3l, 3n, 3o, and 5b demonstrated to be effective inhibitors of PDHc E1 from E. coli and exhibited antifungal activity. SAR analysis indicated that both, the inhibitory potency against E. coli PDHc E1 and the antifungal activity of title compounds, could be increased greatly by optimizing substituent groups in the compounds. The structures of substituent group in 5-position on the 1,2,3-triazole and 4-position on the benzene ring in title compounds were found to play a pivotal role in both above-mentioned biological activities. Amongst all the compounds, compound 5b with iodine in the 5-position of 1,2,3-triazole and with nitryl group in the 4-position of benzene ring acted as the best inhibitor against PDHc E1 from E. coli. It was also found to be the most effective compound with higher antifungal activity against Rhizoctonia solani and Botrytis cinerea at the dosage of 100 ?g mL(-1). Therefore, in this study, compound 5b was used as a lead compound for further optimization.
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