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1.
The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, , CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated. RJC02337相似文献
2.
本文研究了枯草杆菌AS1.398发酵培养制备中性蛋白酶,对发酵培养基配比,培养条件,金属离子的影响等进行了摇瓶试验。制备的AS1.398中性蛋白酶有如下性质:最适PH7.2-7.4,在PH6.5-8.0稳定。最适温度42-44℃,35℃下处理2小时能保持约85%酶活力,60℃下10分钟酶完全失活,此酶被EDTA和Cu2+所抑制 相似文献
3.
L. G. Mezhlumyan Sh. Kh. Rakhimova P. Kh. Yuldashev N. K. Aikhodzhaeva M. A. Saidkhodzhaeva A. I. Massino S. Makhmudova 《Chemistry of Natural Compounds》2004,40(1):59-62
The glutelin fraction was used as the food value index of local corn. The base-soluble fraction was used as a test of the glassiness of local strains of rice grain. The content of gliadins and glutelins did not change over 24 h after wheat grain cultivated in Uzbekistan was moistened. 相似文献
4.
A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization. 相似文献
5.
A. V.?Nemukhin B. L.?Grigorenko A. V.?Rogov I. A.?TopolEmail author S. K.?Burt 《Theoretical chemistry accounts》2004,111(1):36-48
A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH3(NHCO-CH2)2 – HN–CO–(CH2–NHCO)CH3 the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor. 相似文献
6.
7.
An alkalophilic hyperproducer of alkaline protease, Bacillus sp. NG312, was isolated, and the enzyme showed maximum activity at pH 11.0 and 60°C. The temperature optimum was increased
by 10°C in presence of Ca2+. The crudeenzyme was found to have half-life of 11 d at 37°C and maximum stability at pH 9.0–10.0. It also exhibited very
good stability in presence of detergent components and some locally available commericial detergent powders. 相似文献
8.
Robert M. Smith Ping Yuan David P. Weiner Caryn R. Dutton David E. Hansen 《Applied biochemistry and biotechnology》1994,47(2-3):329-343
We describe here a novel strategy for the isolation of antibodies with sequence-specific protease activity: the synthesis
of dipeptide haptens in which the targeted peptide bond has been replaced by a ring-strained or torsionally strained hydroxyethylene
transition-state analog. Thus, the analogs mimic both a peptide bond in a distorted, reactive conformation and the transition
state for peptide bond hydrolysis. In order to obtain sequence-specific antibody proteases, these analogs have been flanked
with additional amino acid residues in preparation for immunization. In particular, we have synthesized peptides containing
analogs such as 2-cis-amino-3-cis-hydroxycyclobutane carboxylic acid andendo-(3-amino-2-hydroxy)bicyclo[2.2.1]heptane-7-anti-carboxylic acid. We have also prepared a series of peptide derivatives containing
analogs, such as 2-[3-amino-2-oxo-1-azetidinyl]-3-methylbutanoic acid, in which the targeted peptide bond has been incorporated
into a β-lactam ring. Since the “peptide bond” has been left intact, these species mimic only a distorted ground state. At
present, antibodies are being elicited against a number of the above peptide derivatives. 相似文献
9.
Pablo A. Molina R. Steven Sikorski Jan H. Jensen 《Theoretical chemistry accounts》2003,109(3):100-107
The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated
by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 Nδ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due
to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore,
the unusual down-field shift of Hɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously
postulated. The free-energy cost of moving Hδ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol.
Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003
Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American
Chemical Society, 2001
Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu
Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the
Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the
NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors
are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions. 相似文献
10.
Observations of the activity of two hydrolyzing enzymes—protease and α-amylase—entrapped inside the reversed micelles formed
by surfactants in hexane, benzene, and cyclohexane are reported. The surfactants chosen for this study are: Tween 80, a nonionic
surfactant, Cetyl pyridinium chloride, a cationic surfactant, and two anionic surfactants, sodium lauryl sulfate and Aerosol
OT.
Tween 80 enhances the activity of both protease and α-amylase. Sodium lauryl sulfate and Aerosol OT, which are ionic surfactants,
enhance the activity of protease, but inhibit the activity of α-amylase. Cetyl pyridinium chloride, however, enhances the
activity of α-amylase, but inhibits the activity of protease. Enhanced activity is generally severalfold greater in comparison
to the activity observed in the usual aqueous system in the absence of reversed micelles. It has also been observed that the
enhanced activity of the enzymes entrapped inside the reversed micelles remains preserved for a much longer period of time
in comparison to the activity in the usual aqueous systems. These observations, which support the view that with proper choice
of surfactant and the organic solvent, reversed micelles act like a microreactor that provides a favorable aqueous microenvironment
for enzyme activity, have biotechnological overtones. 相似文献