WORKPLAN
Workpackage 6
WP6 Docking simulation of neurimidinase inhibitors
WP LEADER HELSINGIN YLIOPISTO
Objectives
The work will involve creating a virtual ligand library and performing ligand neuraminidase docking calculations to predict interactions.
Description of work
The work will involve standard computational technique carried out with facilities of computational time in cluster of computers by a single postdoctoral co-worker. In this workpackage, two different task will be realized.
Task 1: Create a model for neuraminidase inhibitors. Initial efforts will be directed towards the implementation of an efficacy and selective program capable to predict docking of neuraminidase inhibitors.
Task 2: Binding modes of NA inhibitors with Docking simulation. A Binding mode of the synthesized molecule will be examined in order to gain information, based also on the screening test of cells and animals, about the efficacy of the compounds. Based on the findings, creation of the virtual library will mainly proceed by analysis of the active site and identification of sites necessary for ligand binding. Molecular fragments are selected to be docked into these sites. The docked fragments are linked together thus building molecular skeletons. Atom modification to create optimal binding capacity will be done. Synthesis and in silico design will work interactively and rely on continuous feedback. Other inhibitors will be selected and the best binding ligands will be synthesized for experimental testing of activity. Once a plausible set of prime ligand candidates has been defined the databases and synthesis design software available in the laboratories are used in retro synthetic analysis to create detailed synthetic schemes for each candidate
Deliverables
A Single report (D11), at month 36, will be provided detailing with the characterization and results obtained in the in silico screening. Aspect of this deliverable will be presented in the public domain via the web interface and the scientific part of the project symposia (D16)