Advances in Combinatorial Chemistry and High Throughput Screening: Volume 1

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Advances in Combinatorial Chemistry and High Throughput Screening: Volume 1
Copyright
Contents
Foreword
Preface
List of Contributors
1. Assessing Chemicals Using Partial Order Ranking Methodology
	1. Introduction
	2. Methods
		2.1. Partial Order Ranking
		2.2. Linear Extensions
		2.3. Average Ranks
		2.5. Hierarchical POR
		2.6. Accumulating Partial Order Ranking
			2.6.1. Probabilities Based on Accumulated Ranks
		2.7. Quantitative Structure-Activity Relationships
	3. Results
		3.1. The Simple Approach
		3.2. Relative Descriptor Importance
		3.3. Hierarchical Partial Order Ranking
		3.4. Accumulating Partial Order Ranking
	4. Discussion
	5. Conclusions and Outlook
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
2. Building a Chemical Space Based on Fragment Descriptors
	Abstract
	1. Introduction
	2. Types of Fragment Descriptors
	3. Application of Fragment Descriptors in Virtual Screening and in Silico Design
		3.1. Filtering
		3.2. Similarity Search
		3.3. SAR/QSAR/QSPR Models
		3.4. In Silico Design
	Conclusion
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
3. Fluorescent Probes for Cellular Assays
	Abstract
	Introduction
	Kinases
	GPCRs
	Ion Channels
	Cellular Pathway Analysis
	Multiplexing
	Conclusion
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
4. Label-Free Cell Phenotypic GPCR Drug Discovery
	Ye Fang*
	Abstract
	GPCR Signals
	GPCR Oligomerization
		Ligand-Directed Functional Selectivity
	Label-Dependent Cell-Based Assays
		Assays to Measure Changes in Second Messenger
		Assays to Measure Protein Trafficking
		Assays to Measure Protein-Protein Interaction
		Assays to Measure Changes in Gene Reporter Activity
		Assays to Measure Changes in Phenotype
	Label-Free Cell-Based Assays
		RWG Biosensors and Systems
		Electrical Biosensors and Systems
		Optical Signals of GPCR Activation with RWG Biosensor
		Bioimpedance Signals of GPCR Activation
	Label-Free Cell-Based Assays for GPCR Screening
		Receptor Panning
		Systems Cell Biology Studies of GPCR Signaling
		Ligand Pharmacological Profiling
		High Throughput Screening
	Choise of Assay Platforms for GPCR Screening
	Conclusion
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
5. Immunological Assays: Biotools for High Throughput Screening and Characterisation of Combinatorial Libraries
	Abstract
	Introduction
	The Antibody Molecule
	Antibody Engineering
		Genetic and Combinatorial Tools
	BIological Combinatorial Libraries
		Phage Display
		Yeast Surface Display
	Chemical Combinatorial Libraries
		Peptides
		Biomimetic Ligands
	Immunological Methods
		HTS Tools for the Selection of Lead Ligands
		ELISA-Based Methods
	Conclusion
	Abbreviations
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
6. Screening and Mechanism-Based Evaluation of Estrogenic Botanical Extracts
	Abstract
	Introduction
	Materials and Methods
		Plant Material
		Extraction
		ER and ER Competitive Binding Assays
		Cell Culture Conditions
		Induction of Alkaline Phosphatase in Cultured Ishikawa Cells
		Cytotoxicity Assay
		Measure of ERE Activation
	Results
		ER Alpha and ER Beta Competitive Assay
		Estrogenic Alkaline Phosphatase Induction in the Ishikawa Cell Line
		ERE-Luciferase Induction in ER Alpha and ER Beta Positive Cell Lines
	Discussion
	Abbreviations
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
7. A Homogeneous Platform to Discover Inhibitors of the GoLoco Motif/G-alpha Interaction
	Abstract
	Introduction
	Materials and Methods
		Chemicals and Assay Material
		Protein Expression and Purification
		Peptide Synthesis
		Fluorescence Polarization Measurements in 96-Well and 384-Well Plate Formats
		Surface Plasmon Resonance (SPR) Binding Assay
		qHTS Validation in 1,536-Well Plate Format
	Results
		Detection of G /GoLoco Motif Interactions Using Fluorescence Polarization
		Competitive Binding Studies
		Estimation of Screening Window
		Initial Small Molecule Screen in 96-Well Plate Format
		Screening in the 384-Well Plate Format and Hit Validation by SPR
		Assay Miniaturization to 1,536-Well Plates and Evaluation of Red-Shifted Peptide Probes
		qHTS Robotic Validations Using the LOPAC1280 Library
	Discussion
		Sensitivity of Binding Detection and Screening Window Optimization
		Small-Scale Library Screens and Strategies for Minimizing Compound Interference
		Benefits of the qHTS Approach
	Acknowledgement
	Conflict of Interest
	Data Deposition
	Disclosure
	References
8. G-Protein Activation State-Selective Binding Peptides as New Tools for Probing Heterotrimeric G-protein Subunit Signaling Dynamics
	Abstract
	Introduction
	Screening Methods
	Biochemical Insights
		KB-752 – a Gα ·GDP-Selective Phage-Display Peptide
		KB-1753 and Two Other Peptide Families with Affinity for Activated Gα Subunits
		Derivatives of the GoLoco Motif
		Gβγ-Interacting Peptides
	Structural Insights
		KB-752/Gαi1·GDP Complex
		KB-1753/Gαi1·GDP·AlF4- Complex
		SIGK/Gβ1γ2 Complex
	Application in High-Throughput Screening for GPCR Modulators
	Concluding Remarks
	Abbreviations
	Acknowledgement
	Conflict of Interest
	Disclosure
	References
Index
	A
	B
	C
	D
	E
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