@article { ISI:000319221500007, title = {Molecular dynamics simulation studies of the structural response of an isolated A beta(1-42) monomer localized in the vicinity of the hydrophilic TiO2 surface}, journal = {European Biophysics Journal}, volume = {42}, number = {6}, year = {2013}, month = {JUN}, pages = {487-494}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

We have probed the effect of a model hydrophilic surface, rutile TiO2, on the full-length amyloid beta (A beta(1-42)) monomer using molecular dynamics simulations. The rutile surface brings about sharp changes in the peptide{\textquoteright}s intrinsic behavior in a distance-dependent manner. The intrinsic collapse of the peptide is disrupted, while the beta-sheet propensity is sharply enhanced with increased proximity to the surface. The results may have implications for A beta self-assembly and fibrillogenesis on hydrophilic surfaces and should be taken into consideration in the design of novel nanomaterials for perturbing amyloidogenic behavior.

}, keywords = {Amyloid beta, beta-Sheet propensity, molecular dynamics simulation, TiO2 rutile surface}, issn = {0175-7571}, doi = {10.1007/s00249-013-0900-6}, author = {Jose, Jaya C. and Sengupta, Neelanjana} } @article { ISI:000343016000001, title = {Microscopic hydration properties of the a beta(1-42) peptide monomer and the globular protein ubiquitin: a comparative molecular dynamics study}, journal = {Journal of Physical Chemistry B}, volume = {118}, number = {40}, year = {2014}, month = {OCT}, pages = {11591-11604}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Atomistic molecular dynamics simulations of eight selected conformations of a disordered protein amyloid beta (1-42) (A beta), and a globular protein, ubiquitin(UBQ), have been carried out in aqueous media at 310 K. Detailed analyses were carried out to compare the microscopic properties of water molecules present in the hydration layers of these systems. It is notices that irrespective of the conformational heterogeneity among the A beta monomers, water molecules hydrating UBQ. Importantly, the conformational heterogeneity of the A beta monomers has been found to affect the translational and rotational motions of hydration water molecules in a nonuniform manner. Detailed investigation of the timescale of hydrogen bond relaxations at the surface and their energetics revealed the possibility of heterogeneous confinement around different A beta conformations. The distribution of water density fluctuation around A beta conformations are broader compared density fluctuation among the A beta monomers suggests that the structural propensities could affect the peptides effective surface hydrophobicity.

}, issn = {1520-6106}, doi = {10.1021/jp505629q}, author = {Jose, Jaya C. and Khatua, Prabir and Bansal, Nupur and Sengupta, Neelanjana and Bandyopadhyay, Sanjoy} } @article { ISI:000342687200060, title = {Molecular investigations of protriptyline as a multi-target directed ligand in alzheimer{\textquoteright}s disease}, journal = {Plos One}, volume = {9}, number = {8}, year = {2014}, month = {AUG}, pages = {e105196}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is a complex neurodegenerative disorder involving multiple cellular and molecular processes. The discovery of drug molecules capable of targeting multiple factors involved in AD pathogenesis would greatly facilitate in improving therapeutic strategies. The repositioning of existing non-toxic drugs could dramatically reduce the time and costs involved in developmental and clinical trial stages. In this study, preliminary screening of 140 FDA approved nervous system drugs by docking suggested the viability of the tricyclic group of antidepressants against three major AD targets, viz. Acetylcholinesterase (AChE), beta-secretase (BACE-1), and amyloid beta (A beta) aggregation, with one member, protriptyline, showing highest inhibitory activity. Detailed biophysical assays, together with isothermal calorimetry, fluorescence quenching experiments, kinetic studies and atomic force microscopy established the strong inhibitory activity of protriptyline against all three major targets. The molecular basis of inhibition was supported with comprehensive molecular dynamics simulations. Further, the drug inhibited glycation induced amyloid aggregation, another important causal factor in AD progression. This study has led to the discovery of protriptyline as a potent multi target directed ligand and established its viability as a promising candidate for AD treatment.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0105196}, author = {Bansode, Sneha B. and Jana, Asis K. and Batkulwar, Kedar B. and Warkad, Shrikant D. and Joshi, Rakesh S. and Sengupta, Neelanjana and Kulkarni, Mahesh J.} }