Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors

The docking studies and comparative molecular field analysis (CoMFA) were performed on highly active molecules of curcumine derivatives against 3′ processing activity of HIV-1 integrase (IN) enzyme. The optimum CoMFA model was selected with statistically significant cross-validated r² value of 0.815 and non-cross validated r ² value of 0.99. The common pharmacophore of highly active molecules was used for screening of HIV-1 IN inhibitors. The high contribution of polar interactions in pharmacophore mapping is well supported by docking and CoMFA results. The results of docking, CoMFA, and pharmacophore mapping give structural insights as well as important binding features of curcumine derivatives as HIV-1 IN inhibitors which can provide guidance for the rational design of novel HIV-1 IN inhibitors.     

Measurement of sensitivities for the thermal recording of laser beams

A simple technique for determining the energy sensitivities for the thermographic recording of laser beams is described. The principle behind this technique is that, if a laser beam with a known spatial distribution such as a Gaussian profile is used for imaging, the radius of the thermal image formed depends uniquely on the intensity of the impinging beam. Thus by measuring the radii of the images produced for different incident beam intensities the minimum intensity necessary (that is, the threshold) for thermographic imaging is found. The diameter of the laser beam can also be found from this measurement. A simple analysis based on the temperature distribution in the laser heated material shows that there is an inverse square root dependence on pulse duration or period of exposure for the energy fluence of the laser beam required, both for the threshold and the subsequent increase in the size of the recording. It has also been shown that except for low intensity, long duration exposure on very low conductivity materials, heat losses are not very significant.     

The infrared and laser Raman spectra of K2Zn(SO4)2 · 6H2O

The Raman spectra of the single crystal of K₂Zn(SO₄)₂·6H₂O belonging toC _2h ⁵ space group in the 40–1200 cm⁻¹ region in different scattering geometries and their spectra ofthe microcrystalline salt in the 1500-50 cm⁻¹ region have been reported. The dynamics of the crystal has been described in terms of 186 phonon modes under the unit cell approximation. The weak bands in the region 400–900 cm⁻¹ have been assigned to the libratory modes of H₂O molecules in contradiction to the assignments reported by Ananthanarayanan. The ambiguities existing in the literature about the assignments ofν ₂ ^c andν ₅ ^c modes of [Zn(H₂O)₆]²⁺ have also been removed. The translatory and libratory modes of different units of the crystal have been identified and assignments are made using farir and Raman data on various isomorphous tutton salts. It has been inferred that both SO ₄ ²⁻ tetrahedron and [Zn(H₂O)₆]²⁺ octahedron undergo linear as well as angular distortions from their free state symmetries in the crystal.     

A new pivot selection rule for the network simplex algorithm

We present a new network simplex pivot selection rule, which we call theminimum ratio pivot rule, and analyze the worst-case complexity of the resulting network simplex algorithm. We consider networks withn nodes,m arcs, integral arc capacities and integral supplies/demands of nodes. We define a {0, 1}-valued penalty for each arc of the network. The minimum ratio pivot rule is to select that eligible arc as the entering arc whose addition to the basis creates a cycle with the minimum cost-to-penalty ratio. We show that the so-defined primal network simplex algorithm solves minimum cost flow problem within O(nΔ) pivots and in O(Δ(m + n logn)) time, whereΔ is any upper bound on the sum of all arc flows in every feasible flow. For assignment and shortest path problems, our algorithm runs in O(n ²) pivots and O(nm +n ² logn) time.     

Isolation of a Dosage Dependent Lethal Mutation in Ubiquitin Gene of Saccharomyces Cerevisiae

Summary: Ubiquitin is a small protein with a highly conserved sequence, playing a pivotal role in ubiquitin proteasome system (UPS). Considering the central role UPS has in cellular homeostasis, several drugs have been developed to target UPS to remove cells responsible for cancer and other neurodegenerative diseases. As an alternative to the above approach, in the present study we have isolated dose dependent lethal form of ubiquitin gene by in vitro evolution. In vitro evolution is a powerful tool for developing proteins with novel and desirable properties. The ubiquitin gene of Saccharomyces cerevisiae was subjected to in vitro evolution and lethal mutations were selected. The ubiquitin of S. cerevisiae differs only by three residues from human ubiquitin. The mutants were selected by expressing the protein in temperature sensitive ubi4 deletion mutants of ubiquitin. Most of the mutations in ubiquitin gene failed to complement UBI4 phenotype under heat shock. Only one of the mutants caused cell lysis, even at permissive temperature. Interestingly, expression of the same protein in wild type S. cerevisiae cells left them unaffected, establishing the mutant protein as a competitive inhibitor for UPS. Sequencing of the mutant gene showed four completely novel amino acid substitutions. They are namely, Ser20 to Phe, Ala46 to Ser, Leu50 to Pro and Ile61 to Thr. Construction of the mutant ubiquitin gene and characterization of the mutant phenotype along with the nature and location of the mutations are presented.     

Studies on structural and optical properties of pure and transition metals (Ni,Fe and co-doped Ni–Fe) doped tin oxide (SnO2) nanoparticles for anti-microbial activity

Research on Chemical Intermediates - In this present work, pure and transition metal ions (Ni, Fe and co-doped Ni–Fe) doped SnO2 nanoparticles (NPs) were synthesized using a simple chemical...     

Synthesis of novel benzo naphtho naphthyridines from 2,4-dicloroquinolines

A schematic study on the condensation of 2,4-dichloroquinolines ( 1 ) with 1-naphthyamine ( 2 ) in the presence of CuI as a catalyst to functionalized mono ( 3 ) and di ( 4 ) substituted naphthylamino quinolines was described. Consequently, these mono- and di-substituted amines on polyphosphoric acid-catalyzed cyclization reaction with p-toluic acid and acetic acid to yield the linear benzo[b]naphtho[2,1-g][1,8]naphthyridines ( 5 ) and angular benzo[b]naphtho[2,1-h] naphthyridines ( 6 ) in good yields. In addition to descried the similar synthesis of benzo[g]naphtho [2,1-b][1,8]naphthyridines ( 12 ) and benzo[h]naphtho[2,1-g][1,8]naphthyridines ( 13 ) from 2,4-dichlorobenzo[h]quinoline ( 8 ) with various anilines ( 9 ) through my intermediates ( 10 and 11 ).     

QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states

The catalytically active (Ni-SI and Ni-R) and inactive states (Ni-A and Ni-B) of Ni-Fe hydrogenases have been studied using density functional theory (DFT) methods. Both isolated clusters and clusters embedded in the enzyme have been used to model the Ni-A, Ni-B, Ni-SI and Ni-R states. The BP86 and B3LYP functionals were employed, and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods were used for the embedded calculations. The QM/MM studies, rather than the isolated cluster calculations, were generally found to give structures which correlated better with X-ray data. The structure of the unready state (Ni-A), was correctly predicted by the QM/MM, but not by the isolated cluster calculation. Comparison with the observed crystal structure favoured the catalytically active state, Ni-SI, to be the protonated (Ni-SI(II)), rather than the unprotonated state (Ni-SI(I)). In the QM/MM studies, the binding of H(2) to Ni-SI(II) is preferred at the Ni (Ni-R(Ni)), rather than at the Fe centre (Ni-R(Fe)), in agreement with xenon binding studies, and in contrast to isolated cluster studies. These calculations cannot say with certainty which functional should be favoured, nor the preferred spin state of the catalytically active species. However, the lack of any predicted structure in which H(2) binds to the Fe centre, does favour a low spin state for Ni-SI(II), and the use of the BP86 functional. This is in agreement with recent high level ab initio calculations of a model of the Ni-SI(I) state.