CHOLINERGIC LIGAND INTERACTIONS

By Q. ALMID

CONTENTS PART I CHEMICAL SPACE INVESTIGATION OF THE CLICK-CHEMICAL SPACE FOR DRUG DESIGN USING ZINCLICK MOLECULAR SCAFFOLD HOPPING VIA HOLISTIC MOLECULAR REPRESENTATION PART II HIT IDENTIFICATION AND HIT-TO-LEAD OPTIMIZATION BIASED DOCKING FOR PROTEIN–LIGAND POSE PREDICTION BINDING MODE PREDICTION AND VIRTUAL SCREENING APPLICATIONS BY COVALENT DOCKING LIGAND–RECEPTOR INTERACTIONS AND DRUG DESIGN SIMULATION OF LIGAND TRANSPORT IN RECEPTORS USING CAVERDOCK NEGATIVE IMAGE-BASED SCREENING: RIGID DOCKING USING CAVITY INFORMATION NEGATIVE IMAGE-BASED RESCORING: USING CAVITY INFORMATION TO IMPROVE DOCKING SCREENING FRAGMENT-BASED DRUG DESIGN OF SELECTIVE HDAC6 INHIBITORS A PROTOCOL TO USE COMPARATIVE BINDING ENERGY ANALYSIS TO ESTIMATE DRUG-TARGET RESIDENCE TIME DYNAMIC DOCKING USING MULTICANONICAL MOLECULAR DYNAMICS: SIMULATING COMPLEX FORMATION AT THE ATOMISTIC LEVEL FREE ENERGY CALCULATIONS FOR PROTEIN–LIGAND BINDING PREDICTION EXPLOITING WATER DYNAMICS FOR PHARMACOPHORE SCREENING MARKOV STATE MODELS TO ELUCIDATE LIGAND BINDING MECHANISM PART III DRUG REPURPOSING, POLYPHARMACOLOGY, AND TARGET IDENTIFICATION FROM HOMOLOGY MODELING TO THE HIT IDENTI?CATION AND DRUG REPURPOSING: A STRUCTURE-BASED APPROACH IN THE DISCOVERY OF NOVEL POTENTIAL ANTI-OBESITY COMPOUNDS MULTIPLE TARGET DRUG DESIGN USING LIGBUILDER 3 BIONOI: A VORONOI DIAGRAM-BASED REPRESENTATION OF LIGAND-BINDING SITES IN PROTEINS FOR MACHINE LEARNING APPLICATIONS MDOCK: A SUITE FOR MOLECULAR INVERSE DOCKING AND TARGET PREDICTION