Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

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, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}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.     

Spectrophotometric Study of Luminol in Dimethyl Sulfoxide–Potassium Hydroxide

The spectrophotometric study of luminol (LH₂) in dimethyl sulfoxide (DMSO), DMSO-water solutions, and alkaline DMSO and DMSO-water solutions has been done, focusing on the effect of the KOH additon on LH₂ absorption and fluorescence properties. The absorption spectra indicate an acid-base equilibrium, and the luminol dianion (L^2–) formation at 3 × 10^–4 – 2.4 × 10^–3 M KOH. The decrease of the fluorescence intensity and the variation of the excitation spectra of LH₂-DMSO-KOH solutions with KOH concentration have been similarly explained. The acid-base process is reversible. The addition of HCl to the solution with 3.0 × 10^–3 M KOH leads to an increase of the fluorescence intensity to its highest value, observed in pure DMSO. The addition of HCl to the LH₂-DMSO solution leads to the decrease of the fluorescence intensity as a result of the LH⁺ ₃ cation formation. In LH₂-DMSO-water, the fluorescence band is shifted from 405 nm to 424 nm and increased in the intensity. In the presence of KOH (in LH₂-DMSO-water-KOH solution) a new band appears, with the maximum at 485 nm and the band at 405 nm decreased. The changes in fluorescence lifetimes also evidence the different chemical species formed.     

Tetradecanol dehydrogenation over CuO catalyst supported on BaO, CaO and MgO

Bimetallic Cu/Mg, Ca, Ba mixed oxide compounds acted as catalyst in the dehydrogenation of tetradecanol into tetradecanal, and were characterized by thermal gravimetric analysis, surface area, X-ray diffraction, temperature-programmed reduction and desorption of CO₂. Alkaline earth oxides increased the total basic site concentration in the order of Mg>Ca>Ba. A correlation was found between the total basic site concentration and initial dehydrogenation rate. This revised version was published online in June 2006 with corrections to the Cover Date.     

Ratio of Protein Fractions in Cereal Grains Cultivated in Uzbekistan

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.     

Dynamic Interfacial Tension Behavior of Water/Oil Systems Containing In situ-Formed Surfactants

Time-dependent interfacial tension (IFT) has been investigated for an interfacially reactive immiscible system composed of model-acidified oil and alkaline water. The acidified oil was composed of either lauric acid or linoleic acid dissolved in n-dodecane. Drop volume tensiometry was employed to measure the interfacial tension between the two phases. In the case of lauric acid, the IFT value was found to decrease sharply with increasing alkali concentration, even at low drop formation times. In the case of linoleic acid, the IFT decrease with the drop formation time was more gradual, especially at low alkali concentration. The rate of formation of the interfacial area was also found to be dependent on alkali concentration.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

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.     

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

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.