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.     

Computation of triple differential cross-sections with the inclusion of exchange effects in atomic K-shell ionization by relativistic electrons for symmetric geometry

The triple differential cross-section for K-shell ionization of silver and copper atoms by relativistic electrons have been computed in the coplanar symmetric geometry with the inclusion of exchange effects following the multiple scattering theory of Das and Seal [1] multiplied by suitable spinors. Present computed results are marginally improved in some cases from the previous computed results [2]. Present results are compared with measured values [3] and with previous computation results [2]. Some other theoretical computational results are also presented here for comparison.      

Fluorine incorporation in silica glass by the MCVD process: Study of fluorine incorporation zone,evaluation of optical properties and structure of the glass

A theoretical approach was made to find out a complete fluorine incorporation zone on a ternary diagram which serves as a useful graphical representation to select the flows of the supplied reagents for incorporation of the suitable amount of fluorine into cladding glass of optical fiber preform made by the MCVD process using CCl₂F₂ as a source of fluorine under oxygen abundance, oxygen deficiency and intermediate oxygen state conditions. The possible mechanism for incorporation of fluorine into cladding glass of optical fiber is also evaluated on the basis of the thermodynamical data. The fluorine incorporation mechanism in silica glass by the MCVD process is found to be dependent on the CCl₂F₂/SiCl₄ ratio in the input gas mixture. Fluorine doping is found to be effective for removing the strained Si–O–Si bonds, which govern the optical transparency in deep ultra-violet (DUV) and vacuum ultra-violet (VUV) regions. The maximum refractive index depression of ?0.5 × 10^?3 is obtained with incorporation of fluorine into silica cladding glass by the MCVD process using CCl₂F₂ as a dopant precursor with suitable flow of SiCl₄ vapor along with O₂ through backward deposition pass. The structure of fluorine doped silica glass preform samples containing 1.70–1.79 mol% fluorine incorporated by the MCVD process based on the analyses of ¹⁹F MAS spectra done by high-resolution ¹⁹F NMR spectroscopy reveal the presence of two distinct types of fluorine environments. The majority of the fluorine environments are formed in SiO_1.5F polyhedral and less abundant species is observed to be highly unusual, yielding a fivefold coordinated silicon of the type SiO₂F polyhedral which become increased with increasing the fluorine content.     

Lattice instability in Hf1-x Ta x V2 compounds

The temperature dependence of the electric quadrupole interaction frequency _l ^o , experienced by the¹⁸¹Ta probe occupying Hf site in the compounds Hf_1-xTa_xV₂ has been measured for x=0.06, 0.10 and 0.20 in the temperature region between 8.5 K to 296 K. The measurements show lattice transformation in all the three compounds below 120 K.     

Thermal Studies on Ionic Derivatives of Hafnium(IV) Involving Maltol Ligand

A number of ionic chelate complexes of maltol(A) and hafnium(IV) the type[(η₅−C₅H₅)₂HfL]⁺[MCl3]⁻ (B) [HL=maltol; M=Zn(II), Cd(II), Hg(II), Cu(II)]have been synthesized and characterized by spectral studies (IR, UV, ¹H NMR and ¹³C NMR). The stoichiometry of the complexes has been confirmed by conductance measurements. Thermogravimetric (TG) and differential thermal analytical (DTA) studies have been carried out for these complexes and from TG curves, the order, apparent activation energy and apparent activation entropy of the thermal decomposition reactions have been elucidated .The order in each case has been determined to be one and the degree of spontaneity and lability have been inferred from the apparent activation energy and entropy, respectively. Thermal parameters have been correlated with some structural aspects of the complexes concerned. From differential thermal analysis curves, the heat of reaction has been calculated. This revised version was published online in August 2006 with corrections to the Cover Date.     

Ternary copper complexes for photocleavage of DNA by red light: direct evidence for sulfur-to-copper charge transfer and d-d band involvement

A new class of ternary copper(II) complexes of formulation [Cu(L(n)B](ClO(4)) (1-4), where HL(n) is a NSO-donor Schiff base (HL(1), HL(2)) and B is a NN-donor heterocyclic base viz. 1,10-phenanthroline (phen) and 2,9-dimethyl-1,10-phenanthroline (dmp), are prepared, structurally characterized, and their DNA binding and photocleavage activities studied in the presence of red light. Ternary complex [Cu(L(3))(phen)](ClO(4)) (5) containing an ONO-donor Schiff base and a binary complex [Cu(L(2))(2)] (6) are also prepared and structurally characterized for mechanistic investigations of the DNA cleavage reactions. While 1-4 have a square pyramidal (4 + 1) CuN(3)OS coordination geometry with the Schiff base bonded at the equatorial sites, 5 has a square pyramidal (4 + 1) geometry with CuN(3)O(2) coordination with the alcoholic oxygen at the axial site, and 6 has a square planar trans-CuN(2)O(2) geometry. Binding of the complexes 1-4 to calf thymus DNA shows the relative order: phen > dmp. Mechanistic investigations using distamycin reveal minor groove binding for the complexes. The phen complexes containing the Schiff base with a thiomethyl or thiophenyl moiety show red light induced photocleavage. The dmp complexes are essentially photonuclease inactive. Complexes 5 and 6 are cleavage inactive under similar photolytic conditions. A 10 microM solution of 1 displays a 72% cleavage of SC DNA (0.5 microg) on an exposure of 30 min using a 603 nm Nd:YAG pulsed laser (60 mJ/P) in Tris-HCl buffer (pH 7.2). Significant cleavage of 1 is also observed at 694 nm using a Ruby laser. Complex 1 is cleavage inactive under argon or nitrogen atmosphere. It shows a more enhanced cleavage in pure oxygen than in air. Enhancement of cleavage in D(2)O and inhibition with sodium azide addition indicate the possibility of the formation of singlet oxygen as a reactive intermediate leading to DNA cleavage. The d-d band excitation with red light shows significant enhancement of cleavage yield. The results indicate that the phen ligand is necessary for DNA binding of the complex. Both the sulfur-to-copper charge transfer band and copper d-d band excitations helped the DNA cleavage. While the absorption of a red photon induces a metal d-d transition, excitation at shorter visible wavelengths leads to the sulfur-to-copper charge transfer band excitation at the initial step of photocleavage. The excitation energy is subsequently transferred to ground state oxygen molecules to produce singlet oxygen that cleaves the DNA.