In-Silico Drug Discovery and Development.Project: In-Silico Discovery of InfluenzaVirus Polymerase PB1-PB2 ProteinComplex InhibitorsCarla J. Figueroa1,2, Crystal K. Colón1,2Dr. Hector M. Maldonado31RISE Program, 2Univeristy of Puerto Rico at Cayey;3Universidad Central del Caribe, Medical School
2ProblemHypothesisSignificanceCurrent treatment options are limited to Tamiflu and Relenza, withmany reported resistant viral strains.Highly conserved protein-protein interaction interface, present inInfluenza A Virus Polymerase subunits (PB1 and PB2), representpotencial new targets for antiviral drug development.Influenza is an Infectous Disease caused by a virus that kills hundreds ofthousands each year (seasonal epidemics alone), with the iinfluenza-Aserotype implicated in all INF-A related pandemics.
3D Structurewww.pdb.orgPyMol3A1GBioAssaySecondary Screening: (AutoDock)Primary Screening: PharmacophoreModel (ZincPharmer)High AffinityLeadCompoundsIdentification of Top HitsIdentification ofLead Compounds.(Ranking of bindingenergies)Pharmacophoreidentification andPharmacophore ModelGeneration (LigandScout)Therapeuticallyrelevant proteinTargets:PB1-PB2Biological Problem(Influenza Virus)Drug-likeDatabases(17 milliondrug-likecompounds)BenzeneMappingDrug-likeDatabases(17 milliondrug-likecompounds)
Methodology4Software Used:• PyMOL Molecular Graphics System v1.3 http://www.pymol.org• AutoDock (protein-protein docking software) http://autodock.scripps.edu/• Auto Dock Tools: Graphical Interfase for AutoDockhttp://mgltools.scripps.edu/downloads• AutoDock Raccoon: an automated tool for preparing AutoDock virtual screening.http://autodock.scripps.edu/resources/raccoon• AutoDock Vina: improving the speed and accuracy of docking with a new scoringfunction, efficient optimization and multithreading. http://vina.scripps.edu/• LigandScout: Advanced Pharmacophore Modeling and Screening of DrugDatabases. http://www.inteligand.com/ligandscout/Databases Used:• SwissProt/TrEMBL; (Protein knowledgebase and Computer-annotatedsupplement to Swiss-Prot) http://www.expasy.ch/sprot/• National Center for Biotechnology Information (NCBI), Basic Local AlignmentSearch Tool (BLAST) http://www.ncbi.nlm.nih.gov/blast/Blast.cgi• Research Collaboratory for Structural Bioinformatics (RCSB) www.pdb.org• ZINC: A free database for virtual screening: http://zinc.docking.org/
Conclusions• High affinity clusters or “Hot-spots” were identifiedwith benzene mapping• With this information an initial Pharmacophore modelwas developed• This Pharmacophore model was used to perform aprimary screening (filtering) of a large database• 80,231 compounds were identified in that initialscreening that fulfill all requirements of this model• Secondary screening (docking) was performed• The result were organized by binding energy rankingand the top hits identified8