Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR,FB-QSSR,multi objective (MO-QSPR) and MIF studies

The ability to identify fragments that interact with a biological target is a key step in FBDD. To date, the concept of fragment based drug design (FBDD) is increasingly driven by bio-physical methods. To expand the boundaries of QSAR paradigm, and to rationalize FBDD using In silico approach, we propose a fragment based QSAR methodology referred here in as FB-QSAR. The FB-QSAR methodology was validated on a dataset consisting of 52 Hydroxy ethylamine (HEA) inhibitors, disclosed by GlaxoSmithKline Pharmaceuticals as potential anti-Alzheimer agents. To address the issue of target selectivity, a major confounding factor in the development of selective BACE1 inhibitors, FB-QSSR models were developed using the reported off target activity values. A heat map constructed, based on the activity and selectivity profile of the individual R-group fragments, and was in turn used to identify superior R-group fragments. Further, simultaneous optimization of multiple properties, an issue encountered in real-world drug discovery scenario, and often overlooked in QSAR approaches, was addressed using a Multi Objective (MO-QSPR) method that balances properties, based on the defined objectives. MO-QSPR was implemented using Derringer and Suich desirability algorithm to identify the optimal level of independent variables (X) that could confer a trade-off between selectivity and activity. The results obtained from FB-QSAR were further substantiated using MIF (Molecular Interaction Fields) studies. To exemplify the potentials of FB-QSAR and MO-QSPR in a pragmatic fashion, the insights gleaned from the MO-QSPR study was reverse engineered using Inverse-QSAR in a combinatorial fashion to enumerate some prospective novel, potent and selective BACE1 inhibitors.     

Unique asymmetric (CuII4) double-stranded helicate from a hexadentate piperazine-based ligand: ligand conformation isomerism upon coordination

In methanol, the reaction of Cu(ClO(4))(2).6H(2)O and a sterically constrained piperazine imine phenol ligand (H(2)L), in the presence of NEt(3), affords a novel tetranuclear copper(II) complex of formula [Cu(II)(4)(mu(3)-L)(2)(mu-OH)(2)(H(2)O)(2)](ClO(4))(2).H(2)O (1). The X-ray structure of this complex shows an elongated Cu(4) quasi-tetrahedron coordinated to two hexadentate chair-(e,a)-mu(3)-piperazine bridging ligands. Variable-temperature magnetic studies show an S(t) = 0 spin ground state resulting from antiferromagnetic interactions between Cu(II) ions within the complex.     

Interaction of mixed convection in two-sided lid driven differentially heated square enclosure with radiation in presence of participating medium

The current study addresses the mathematical modeling aspects of transport phenomena in steady, two-dimensional, laminar flow accompanied by heat transfer in a lid-driven differentially heated cavity in presence of radiatively absorbing, emitting and scattering gray medium. The walls of the enclosure are considered to be opaque, diffusive and gray. Mixed convection is the outcome of the interaction of forced convection induced by the moving vertical hot and cold wall with the natural convection induced due to the differentially heated enclosure. Two different orientations of the wall movement have been considered to simulate opposing and aiding mixed convection phenomenon and to study its interaction with radiation. Vorticity-stream function formulation of N–S equation has been employed. The discrete ordinate method has been used in modeling the radiative transport equation followed with finite volume method as discretisation technique. The effect of influencing parameters on fluid flow and heat transfer has been studied.     

Parity-violating electron scattering from 4He and the strange electric form factor of the nucleon

We have measured the parity-violating electroweak asymmetry in the elastic scattering of polarized electrons from 4He at an average scattering angle = 5.7 degrees and a four-momentum transfer Q2 = 0.091 GeV2 . From these data, for the first time, the strange electric form factor of the nucleon G(E)s can be isolated. The measured asymmetry of A(PV) = (6.72 +/- 0.84(stat) +/- 0.21(syst) x 10(-6) yields a value of G(E)s = -0.038 +/- 0.042(stat) +/- 0.010(syst), consistent with zero.     

Calcium acetate catalyzed synthesis of 4-arylidene-2-phenyl-5(4H)-oxazolones under solvent-free conditions

Eight 4-arylidene-2-phenyl-5(4H)-oxazolones (azlactones) have been prepared via Erlenmeyer synthesis from aromatic aldehydes and hippuric acid using calcium acetate under solvent-free conditions with microwave irradiation.     

Morse Theory for Filtrations and Efficient Computation of Persistent Homology

We introduce an efficient preprocessing algorithm to reduce the number of cells in a filtered cell complex while preserving its persistent homology groups. The technique is based on an extension of combinatorial Morse theory from complexes to filtrations.     

Discrete Morse Theory for Computing Cellular Sheaf Cohomology

Sheaves and sheaf cohomology are powerful tools in computational topology, greatly generalizing persistent homology. We develop an algorithm for simplifying the computation of cellular sheaf cohomology via (discrete) Morse theoretic techniques. As a consequence, we derive efficient techniques for distributed computation of (ordinary) cohomology of a cell complex.     

Ca2+ INFLUX INDUCED BY PHOTODYNAMIC ACTION IN HUMAN CEREBRAL GLIOMA (U-87 MG) CELLS: POSSIBLE INVOLVEMENT OF A CALCIUM CHANNEL

Abstract The plasma membrane has been implicated as a critical target of photodynamic action on cells. We have observed that the photosensitization of human cerebral glioma (U-87 MG) cells by hematoporphyrin derivative (HpD) causes a large increase in intracellular calcium [Ca²⁺]. This increase in [Ca²⁺]_i was solely due to the influx of extracellular Ca²⁺ through the plasma membrane and showed a dependence on HpD concentration, light dose and concentration of calcium in the extracellular medium. The magnitude of the Ca²⁺ influx decreased with increasing postirradiation time, which suggests that the cell membrane partially recovers from the photodynamic injury. The photoinduced Ca²⁺ influx was inhibited by the Ca²⁺ channel blocker diltiazem and the reducing agent dithioerythritol. These findings are discussed in terms of possible activation of a Ca²⁺ channel as a result of photosensitization.     

Asymmetric synthesis of hydroxy-skipped bishomo-inositols as potential glycosidase inhibitors

Four isomeric hydroxy-skipped bishomo-inositol analogs have been synthesized from both enantiomers of 5-hydroxymethyl-2-cyclohexenone. Sharpless asymmetric dihydroxylation and substrate-directed anionic hydroxymethylation are the key reactions which have been employed successfully for the synthesis of new cyclitols. The synthesized cyclitols have been screened for their inhibitory effect on α- and β-glycosidases.