MOLECULAR BIOLOGY IN MEDICINAL CHEMISTRY
CONTENTS PART I MOLECULAR TARGETS CELLULAR ASSAYS IN DRUG DISCOVERY INTRODUCTION POSITIONING CELLULAR ASSAYS IMPACT ON DRUG DISCOVERY CLASSI?CATION OF CELLULAR ASSAYS PROGRESS IN TOOLS AND TECHNOLOGIES FOR CELLULAR COMPOUND PRO?LING MEMBRANE PROTEINS AND FAST CELLULAR RESPONSES RECEPTORS FLIPR TECHNOLOGY FOR DETECTION OF INTRACELLULAR CALCIUM RELEASE COMPETITIVE IMMUNOASSAY FOR DETECTION OF INTRACELLULAR CAMP ENZYME FRAGMENT COMPLEMENTATION (EFC) TECHNOLOGY MEMBRANE TRANSPORT PROTEINS ION CHANNELS MDR PROTEINS GENE AND PROTEIN EXPRESSION PRO?LING IN HIGH-THROUGHPUT FORMATS REPORTER GENE ASSAYS IN LEAD FINDING REPORTER GENE ASSAYS IN LEAD OPTIMIZATION SPATIO-TEMPORAL ASSAYS AND SUBPOPULATION ANALYSIS PHOSPHORYLATION STAGE-SPECI?C ANTIBODIES TARGET-PROTEIN-SPECI?C ANTIBODIES PROTEIN–GFP FUSIONS FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) GPCR ACTIVATION USING BIOLUMINESCENCE RESONANCE ENERGY TRANSFER (BRET) PROTEIN FRAGMENT COMPLEMENTATION ASSAYS (PCA) PHENOTYPIC ASSAYS PROLIFERATION/RESPIRATION/TOXICITY APOPTOSIS DI?ERENTIATION MONITORING CELL METABOLISM OTHER PHENOTYPIC ASSAYS ACKNOWLEDGMENTS REFERENCES GENE KNOCKOUT MODELS GENE KNOCKOUT MICE ES CELLS TARGETING VECTOR SELECTION OF RECOMBINANT ES CELLS INJECTION OF RECOMBINANT ES CELLS INTO BLASTOCYSTS AND BLASTOCYST TRANSFER TO PSEUDOPREGNANT RECIPIENTS CHIMERAS AND F1 AND F2 O?SPRING TISSUE-SPECI?C GENE EXPRESSION LIGAND-ACTIVATED CRE RECOMBINASES THE TETRACYCLINE/DOXYCYCLINE-INDUCIBLE EXPRESSION SYSTEM TRANSGENIC MICE TARGETED GENE DISRUPTION IN DROSOPHILA TARGETED GENE KNOCKDOWN IN ZEBRA?SH TARGETED CAENORHABDITIS ELEGANS DELETION STRAINS REPORTER GENE ASSAY SYSTEMS FOR THE INVESTIGATION OF G-PROTEIN-COUPLED RECEPTORS RECEPTORS AND CELLULAR COMMUNICATION ION CHANNEL-LINKED RECEPTORS ENZYME-LINKED CELL-SURFACE RECEPTORS GPCRS A?NITY AND ACTIVITY OF GPCR LIGANDS THE ROLE OF TRANSCRIPTION FACTORS IN GENE EXPRESSION CREB SRF STAT PROTEINS C-JUN NF-AT REPORTER GENES CAT B-GAL B-GLUCURONIDASE SEAP B-LACTAMASE LUCIFERASE GFP REPORTER GENE ASSAY SYSTEMS FOR THE INVESTIGATION OF GPCRS APPLICATION OF LUCIFERASE AS A REPORTER GENE APPLICATION OF OTHER REPORTER GENES FOR THE INVESTIGATION OF GPCRS FROM THE HUMAN GENOME TO NEW DRUGS: THE POTENTIAL OF ORPHAN G-PROTEIN- COUPLED RECEPTORS GPCRS AND THE HUMAN GENOME GPCR ARCHITECTURE, SIGNALING AND DRUG ACTION IDENTI?CATION OF GPCRS GPCRS IN THE POSTGENOMIC ERA: ORPHAN RECEPTORS LIGAND HUNTING REVERSE PHARMACOLOGY APPROACHES TO OGPCRS IN SILICO APPROACHES TISSUE EXPRESSION EXPRESSION OF AN OGPCR OF INTEREST SCREENING APPROACHES SCREENING FOR OGPCR LIGANDS USING FUNCTIONAL ASSAYS GTPGS-BINDING ASSAYS MEASUREMENTS OF CAMP CA2Þ MEASUREMENTS THE CYTOSENSOR MICROPHYSIOMETER REPORTER GENE ASSAYS GPCR–G-PROTEIN COUPLING LIGAND-INDEPENDENT GPCR ACTIVITY NOVEL SCREENING STRATEGIES FUTURE PROSPECTS PART II SYNTHESIS STEREOSELECTIVE SYNTHESIS WITH THE HELP OF RECOMBINANT ENZYMES STEREOSELECTIVE SYNTHESIS BEFORE THE ADVENT OF GENETIC ENGINEERING CLASSICAL METHODS OF STRAIN IMPROVEMENT FOR STEREOSELECTIVE SYNTHESIS GENETIC ENGINEERING AND THE ADVENT OF RECOMBINANT ENZYMES FOR STEREOSELECTIVE SYNTHESIS B-LACTAM ANTIBIOTICS PENICILLINS CEPHALOSPORINS POLYKETIDE ANTIBIOTICS VITAMINS L-ASCORBIC ACID (VITAMIN C) BIOTIN (VITAMIN B8, VITAMIN H) RIBO?AVIN (VITAMIN B2) NICOTINAMIDE (VITAMIN B3 OR PP) D-PANTOTHENIC ACID (VITAMIN B5) VITAMIN A VITAMIN K (MENAQUINONE) STEROIDS OTHER DRUGS L-DIHYDROXYPHENYL ALANINE (L-DOPA) N-ACETYL NEURAMINIC ACID (NANA) CHOLESTERIN BIOSYNTHESIS INHIBITORS (HMG-COA REDUCTASE INHIBITORS) OMAPATRILAT HYDROMORPHONE CONCLUDING REMARKS NUCLEIC ACID DRUGS CHEMICAL SYNTHESIS OF OLIGONUCLEOTIDES CHEMICAL MODI?CATIONS OF OLIGONUCLEOTIDES 20-MODI?CATIONS ALKYL- AND ARYLPHOSPHONATES PHOSPHOROTHIOATES N30-P50-PHOSPHORAMIDATES MORPHOLINO OLIGONUCLEOTIDES PNAS STERICALLY LNAS OLIGONUCLEOTIDE CONJUGATES 50-END CONJUGATES 30-END CONJUGATES MECHANISM OF ACTION THE ANTISENSE CONCEPT STERIC BLOCKING RNASE H ACTIVATION THE TRIPLEX CONCEPT RIBOZYMES STRUCTURE AND REACTION MECHANISM TRIPLET SPECI?CITY STABILIZATION OF RIBOZYMES INHIBITION OF GENE EXPRESSION COLOCALIZATION RNAI POSITIONING IDENTI?CATION OF RIBOZYME ACCESSIBLE SITES ON TARGET RNA DELIVERY APPLICATION CONCLUSION PART III ANALYSIS RECENT TRENDS IN ENANTIOSEPARATION OF CHIRAL DRUGS CURRENT STATUS IN THE DEVELOPMENT AND USE OF CHIRAL DRUGS THE ROLE OF SEPARATION TECHNIQUES IN CHIRAL DRUG DEVELOPMENT, INVESTIGATION AND USE PREPARATION OF ENANTIOMERICALLY PURE DRUGS RESOLUTION OF RACEMATES CHIRAL POOL CATALYTIC ASYMMETRIC SYNTHESIS CHROMATOGRAPHIC TECHNIQUES SMB OTHER CHROMATOGRAPHIC AND ELECTROPHORETIC TECHNIQUES FOR THE PREPARATION OF ENANTIOMERS BIOANALYSIS OF CHIRAL DRUGS HPLC CEC FUTURE TRENDS AFFINITY CHROMATOGRAPHY PRINCIPLES OF A?NITY CHROMATOGRAPHY THE LIGAND MONOSPECI?C LIGANDS GROUP-SPECI?C LIGANDS LIGAND DEVELOPMENT THE A?NITY MATRIX THE SUPPORT MATERIAL IMMOBILIZATION OF THE LIGAND PRINCIPLES OF OPERATION MODES OF A?NITY CHROMATOGRAPHY BIOA?NITY CHROMATOGRAPHY IMMUNOA?NITY CHROMATOGRAPHY DYE-LIGAND-A?NITY CHROMATOGRAPHY IMMOBILIZED METAL ION-A?NITY CHROMATOGRAPHY (IMAC) HYDROPHOBIC INTERACTION CHROMATOGRAPHY (HIC) COVALENT CHROMATOGRAPHY MEMBRANE A?NITY CHROMATOGRAPHY APPLICATIONS OF A?NITY INTERACTIONS PURI?CATION OF PHARMACEUTICAL PROTEINS PLASMA PROTEINS RECOMBINANT PROTEINS ANALYTICAL APPLICATIONS HPAC A?NITY CAPILLARY ELECTROPHORESIS A?NITY BIOSENSORS NUCLEAR MAGNETIC RESONANCE-BASED DRUG DISCOVERY SAR BY NMR SAMPLE PREPARATION QUANTITATIVE EVALUATION BINDING A?NITIES STRUCTURE DETERMINATION FROM CHEMICAL SHIFT PERTURBATIONS ADVANCED TECHNOLOGIES IN SAR BY NMR DATA EVALUATION MONITORING SMALL MOLECULES RELAXATION METHODS DI?USION METHODS METHODS INVOLVING MAGNETIZATION TRANSFER TRANSFERRED NOE (TRNOE) SATURATION TRANSFER NOE PUMPING WATERLOGSY AND EPHOGSY CONCLUSIONS 13C- AND 15N-ISOTOPIC LABELING OF PROTEINS EXPRESSION SYSTEMS FOR THE IN VIVO INCORPORATION OF 13C AND 15N LABELS INTO PROTEINS PROTEIN PRODUCTION AND 13C AND 15N-LABELING IN E COLI EXPRESSION SYSTEMS 13C- AND 15N-LABELING OF PROTEINS IN P PASTORIS 13C- AND 15N-LABELING OF PROTEINS BY EXPRESSION IN CHINESE HAMSTER OVARY (CHO) CELLS 13C- AND 15N-LABELING OF PROTEINS IN OTHER ORGANISMS STRATEGIES FOR THE PRODUCTION OF SELECTIVELY 13C- AND 15N-LABELED PROTEINS 10 2 5 1 SELECTIVE LABELING OF AMINO ACIDS 10 2 5 2 SPECI?C ISOTOPE LABELING WITH 13C 10 2 5 3 SEGMENTAL ISOTOPE LABELING CELL-FREE ISOTOPE LABELING COMPONENTS OF CELL-FREE EXPRESSION SYSTEMS CELL-FREE EXPRESSION TECHNIQUES SPECI?C APPLICATIONS OF THE CELL-FREE LABELING TECHNIQUE APPLICATION OF ANTIBODY FRAGMENTS AS CRYSTALLIZATION ENHANCERS CRYSTALLIZATION OF MEMBRANE PROTEINS MEDIATED BY ANTIBODY FRAGMENTS OVERVIEW GENERATION OF ANTIBODIES SUITABLE FOR CO-CRYSTALLIZATION 11 2 2 1 IMMUNIZATION 11 2 2 2 SELECTION OF ANTIBODIES 11 2 2 3 ANTIBODY FRAGMENTS PROTEIN PURI?CATION AND CRYSTALLIZATION 11 2 3 1 INDIRECT IMMUNOA?NITY PURI?CATION 11 2 3 2 CRYSTALLIZATION 11 2 3 3 ALTERNATIVE APPROACHES FOR EXPANSION OF THE POLAR SURFACE CONTENTS PART IV KINETICS, METABOLISM AND TOXICOLOGY PHARMACOGENETICS: THE EFFECT OF INHERITED GENETIC VARIATION ON DRUG DISPOSITION AND DRUG RESPONSE GENERAL RELATIONSHIPS BETWEEN GENOTYPE AND PHENOTYPE ESTABLISHING RELATIONS BETWEEN GENOTYPE AND PHENOTYPE PHENOTYPING VERSUS GENOTYPING – PREDICTION OF INDIVIDUAL DRUG RESPONSE GENETIC POLYMORPHISM IN DMES GENETIC POLYMORPHISM IN DRUG TRANSPORTERS MULTIDRUG RESISTANCE GENE – MARKER VERSUS FUNCTIONAL POLYMORPHISM GENETIC POLYMORPHISMS IN DRUG TARGETS CHOLESTEROL ESTER TRANSFER PROTEIN (CETP) POLYMORPHISM AS A BIOMARKER FOR RESPONSE TO LIPID-LOWERING THERAPY B2-ADRENERGIC RECEPTOR: PREDICTABILITY OF HAPLOTYPE VERSUS SINGLE SNPS POLYGENIC DRUG TARGET POLYMORPHISM: RESPONSE TO CLOZAPINE TREATMENT PHARMACOGENOMICS OF BIOAVAILABILITY AND ELIMINATION CONTRIBUTION OF METABOLISM TO DRUG CLEARANCE CYPS 13 2 1 4 CYP3A PHASE II ENZYMES 13 2 2 1 ARYLAMINE N-ACETYLTRANSFERASES (NAT2) 13 2 2 2 THIOPURINE-S-METHYLTRANSFERASE (TPMT) DRUG TRANSPORTERS: P-GLYCOPROTEIN (P-GP) TOXICOGENOMICS: INTEGRATION OF NEW MOLECULAR BIOLOGICAL TOOLS IN TOXICOLOGY DEVELOPMENTS IN TOXICOLOGY FUNCTIONAL GENOMICS: NEW MOLECULAR BIOLOGICAL TOOLS GENOMICS TRANSCRIPTOMICS PROTEOMICS METABOLOMICS DATA PROCESSING AND BIOINFORMATICS BIOLOGICAL INTERPRETATION INTEGRATION OF FUNCTIONAL GENOMICS TECHNOLOGIES IN TOXICOLOGY MECHANISM ELUCIDATION TRANSCRIPTOMICS FINGERPRINTING AND PREDICTION OF TOXICITY IDENTI?CATION OF EARLY MARKERS OF TOXICITY INTERSPECIES EXTRAPOLATION EXTRAPOLATION FROM IN VITRO EXPERIMENTS TO THE IN VIVO SITUATION REDUCTION OF USE OF LABORATORY ANIMALS COMBINATORIAL TOXICOLOGY ILLUSTRATION: THE APPLICATION OF TOXICOGENOMICS TO STUDY THE MECHANISM OF BROMOBENZENE-INDUCED HEPATOTOXICITY