Computational studies to elucidate the role of proteins in the prevention of malaria A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2010 Jaclyn Bibby School of Chemical Engineering and Analytical Science Contents Abstract ........................................................................................................................... 25 Declaration ...................................................................................................................... 26 Copyright Statement ....................................................................................................... 27 Publications from this Thesis. ......................................................................................... 28 1. Introduction ................................................................................................................. 29 1.1 Vector borne diseases ................................................................................................ 30 1.1.1 Malaria ................................................................................................................ 30 1.1.2 Dengue ................................................................................................................ 30 1.2 Vectors ...................................................................................................................... 31 1.2.1 Anopheles ........................................................................................................... 31 1.2.2. Aedes ................................................................................................................. 32 1.3 Insecticide treated nets .............................................................................................. 33 1.4 History of pyrethroid development ........................................................................... 33 1.5 Pyrethroid structure ................................................................................................... 34 1.6 Pyrethroid resistance ................................................................................................. 36 1.6.1 Housefly pyrethroid resistance ........................................................................... 36 1.7 P450s ......................................................................................................................... 37 1.7.1 P450 structure ..................................................................................................... 37 1.7.2 History of P450 structure determination ............................................................ 38 1.7.3 Substrate Recognition Sites (SRS) ..................................................................... 38 1.7.4 Common active site binding ............................................................................... 39 1.7.5 The P450 cycle ................................................................................................... 40 1.7.6 P450 inhibitors ................................................................................................... 43 1.7.7 P450 regulation and induction ............................................................................ 43 1.8 Experimental determination of structure ................................................................... 43 1.8.1 X-ray crystallography ......................................................................................... 44 1.8.2 NMR ................................................................................................................... 45 1.9 Modelling .................................................................................................................. 46 1.9.1 History of P450 structure prediction .................................................................. 47 1.10 Kinetics ................................................................................................................... 48 1.11 Structure based drug design .................................................................................... 49 1.12 Modelling and characterization of mosquito P450s ................................................ 50 2. Method ........................................................................................................................ 52 2.0 Preface ....................................................................................................................... 53 2 2.1 Introduction ............................................................................................................... 53 2.2 Homology modelling ................................................................................................ 53 2.2.1 Template selection .............................................................................................. 54 2.2.2 Sequence identity ............................................................................................... 55 2.2.3 Sequence Alignment ........................................................................................... 56 2.2.4 Secondary structure prediction ........................................................................... 57 2.2.5 BLAST ............................................................................................................... 58 2.2.6 Phylogeny ........................................................................................................... 59 2.2.7 Model Building ................................................................................................... 60 2.2.8 Model evaluation ................................................................................................ 61 2.2.8.1 ERRAT ......................................................................................................... 61 2.3 Docking ..................................................................................................................... 62 2.3.1 GOLD ................................................................................................................. 63 2.3.2 ChemScore ......................................................................................................... 64 2.3.3 DOCK ................................................................................................................. 68 2.3.4 DOCK anchor and grow ..................................................................................... 69 2.3.5 DOCK Scoring ................................................................................................... 69 2.4 Active site solvation .................................................................................................. 71 2.4.1 Solvation with DOWSER ................................................................................... 71 2.4.2 MOE water soak ................................................................................................. 71 2.4.3 GOLD Ligand Docking with water .................................................................... 71 2.5 Model validation ....................................................................................................... 72 2.6 Identification of channels .......................................................................................... 73 2.6.1 MOLE ................................................................................................................. 73 2.7 Protein-protein docking ............................................................................................. 74 2.7.1 GRAMM ............................................................................................................ 74 2.7.2 PatchDock .......................................................................................................... 75 2.7.3 Zdock .................................................................................................................. 76 2.7.4 DOT .................................................................................................................... 77 2.7.5 ClusPro ............................................................................................................... 78 2.7.6 FireDock ............................................................................................................. 79 2.8 Electrostatics ............................................................................................................. 79 2.9 Membrane binding .................................................................................................... 80 2.9.1 MAPAS ............................................................................................................... 80 2.9.2 HotPatch ............................................................................................................. 81 3 2.10 Pharmacophores ...................................................................................................... 81 2.10.1 MOE ................................................................................................................. 82 2.10.2 LigandScout ...................................................................................................... 82 2.10.3 SARvision ........................................................................................................ 82 2.11 Site of metabolism prediction ................................................................................. 82 2.12 Dynamics ...............................................................................................................