Proteomics for Drug Discovery

This book reflects the drug development community's interest in proteomics methods by providing researchers with the necessary knowledge for the implementation of a number of basic experimental and bioinformatics protocols in the drug discovery research laboratory. The focus of the collection is on select protocols and methodologies that address the analysis of post-translational modifications, targeted protein quantification, protein-protein, protein-lipid, or protein-ATP interactions, in silico lead identification, protein arrays, tissue and cell extract preparation, labeling, chemoproteomics, and drug efficacy assessment. Emphasis was placed not just on methods that describe large-scale protein analysis, but also on ones that are amenable to future implementation in a high-throughput format. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates.- Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins.- Monitoring Dynamic Changes of the Cell Surface Glycoproteome by Quantitative Proteomics.- High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics: An Application to Study the Quantitative Changes Induced by Histone Modifying Enzyme Inhibitors and Activators.- Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context ofDrug Target/Biomarker Discovery.- Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules.- Microfluidics-Mass Spectrometry of Protein-Carbohydrate Interactions: Applications to Development of Therapeutics and Biomarker Discovery.- Studying Protein-Protein Interactions by Biotin AP-Tagged Pulldown and LTQ-Orbitrap Mass Spectrometry.- Post-Translational Modification Profiling-Functional Proteomics for the Analysis of Immune Regulation.- Reverse Phase Protein Arrays and Drug Discovery.- Probing Protein Kinase-ATP Interactions Using a Fluorescent ATP Analog.- Preparation of Disease-Related Protein Assemblies for Single Particle Electron Microscopy.- Identification of Lipid-Binding Modulators Using the Protein-Lipid Overlay Assay.- Resazurin Live Cell Assay: Setup and Fine-Tuning for Reliable Cytotoxicity.- Exploring Protein-Protein Interactions as Drug Targets for Anti-Cancer Therapy with In Silico Workflows.- Method to Identify Silent Codon Mutations that May Alter Peptide Elongation Kinetics and Co-Translational Protein Folding.- In Silico Design of Anticancer Peptides.- Docking and Virtual Screening in Drug Discovery.- Bioinformatics Resources for Interpreting Proteomics Mass Spectrometry Data.