Chemical and biochemical approaches for the study of anesthetic function. Part A / edited by Roderic G. Eckenhoff, Ivan J. Dmochowski.

Format:

Book

Contributor:

Eckenhoff, Roderic G., editor.

Dmochowski, Ivan J., editor.

Series:

Methods in enzymology ; Volume 602.

Methods in Enzymology ; Volume 602

Language:

English

Subjects (All):

Anesthetics--Physiological effect.

Anesthetics.

Physical Description:

1 online resource (xvi, 416 pages).

Edition:

First edition.

Place of Publication:

Cambridge, Massachusetts : Academic Press, [2018]

Summary:

Chemical and Biochemical Approaches for the Study of Anesthetic Function, Part A, Volume 602 assembles new information on our understanding of anesthesia. This latest release in the series includes sections on how physical accuracy leads to biological relevance, best practices for simulating ligand-gated ion channels interacting with general anesthetics, computational approaches for studying voltage-gated ion channels modulation by general anesthetics, anesthetic parameterization, pharmacophore QSAR, QM, ONIOM, and kinetic modeling of electrophysiology data.- We have selected the primary experts to write about each approach- This provides one-stop shopping for all the means of addressing this complex question- Anesthesia is enormously important as almost everybody receives it at some point

Contents:

Front Cover

Chemical and Biochemical Approaches for the Study of Anesthetic Function, Part A

Copyright

Contents

Contributors

Preface

Section I: Computational Approaches

Chapter One: Physical Accuracy Leads to Biological Relevance: Best Practices For Simulating Ligand-Gated Ion Channels Int ...

1. Introduction

2. MD Simulation Involving pLGICs

3. Discovery of Candidate Sites

3.1. Flooding Simulation

3.2. Docking

3.3. MD Refinement and Characterization of Specific Interactions

4. Calculation of Absolute and Relative Binding Affinities

5. Summary

References

Chapter Two: Computational Approaches to Studying Voltage-Gated Ion Channel Modulation by General Anesthetics

1. Voltage-Gated Ion Channels

1.1. Structure and Function

1.2. Conduction Cycle and Functional States

1.3. Modulation by General Anesthetics

2. Structural Approaches to Studying Functional States

2.1. Generating Structural Models of Functional States

3. Detection of Binding Sites and Access Pathways

3.1. "Coarse" Molecular Docking Approaches

3.2. Molecular Dynamics Flooding Simulations

3.2.1. Flooding of General Anesthetics on VGICs

3.2.2. Flooding of General Anesthetics on Other Ion Channels

3.3. Binding Mode Hypotheses

3.4. Characterization of Access Pathways

4. Predicting Binding Affinity

4.1. FEP Approach

4.2. Funnel Metadynamics

5. Summary and Future Perspectives

Chapter Three: Molecular Mechanics Parameterization of Anesthetic Molecules

1.1. Molecular Mechanics

1.2. Bonded vs Nonbonded Terms

2. Overview of Parameterization Method

3. Methods for Choosing Parameters

3.1. Implementation Details

3.2. Automatic Parameterization Software

3.3. Creating a Residue Topology With Atom Types and Partial Charges

3.4. Bonds and Angles.

3.5. Dihedrals

3.6. Comparison With Experiment

4. Summary

Acknowledgments

Chapter Four: Insights Into Receptor-Based Anesthetic Pharmacophores and Anesthetic-Protein Interactions

2. Homology Modeling

2.1. Creating a Homology Model of the GABAAR

2.2. Creating an Anesthesia Binding Site Within the hGABAAR Model

2.3. Characterizing the Receptor-Based Pharmacophore of the hGABAAR Model

2.4. Validating the hGABAAR Model and Anesthetic Binding Site

3. Receptor-Based Pharmacophore Based on Anesthetics Complexed With Non-LGIC Proteins

3.1. The Problem With Deriving the Ligand-Based Anesthetic Pharmacophore

3.2. The Available Systems for Examining Anesthetic-Protein Complexes

3.3. The Use of In Silico Computational Chemistry to Reveal the Complex Nature of Anesthetic-Protein Interactions

4. Summary and Conclusions

Chapter Five: Understanding Anesthetic Mechanisms: Analysis of the Complex Kinetics of Ligand-Gated Ion Channels

2. Methods

3. Discussion

4. Conclusions

Acknowledgment

Section II: Genetics and Model Organisms

Chapter Six: General Genetic Strategies

2. Organisms

2.1. Yeast (Saccharomyces cerevisiae)

2.2. Nematodes

2.3. Flies

2.4. Zebrafish

2.5. Mouse

2.6. Human

3. Endpoints

3.1. Yeast (S. cerevisiae)

3.2. Nematodes (C. elegans)

3.3. Fruit Flies (D. melanogaster)

3.4. Mice (Mus musculus)

4. Strategies

4.1. Forward Screens

4.1.1. Mutagenesis

4.1.2. RNAi

4.1.3. Recombinant Inbred Screens

4.2. Targeted Screens

4.2.1. RNAi

4.2.2. Site-Directed Mutagenesis (SDM)

4.2.2.1. Homologous Recombination

4.2.2.2. Cre Recombinase

4.2.2.3. Inducible Cre Recombinase

4.2.2.4. Optogenetics

4.2.2.5. CRISPR/Cas9

References.

Chapter Seven: Approaches to Anesthetic Mechanisms: The C. elegans Model

1.1. Advantages of the Model Organism, C. elegans

1.2. Disadvantages of the Model Organism, C. elegans

2. Exposing Worms to Volatile Anesthetics

2.1. Using Anesthetic Chambers

2.1.1. Equipment and Reagents

2.1.2. Procedure

2.1.3. Notes

2.2. Determining Anesthetic Concentration: Collection of Gas Samples

2.2.1. Equipment

2.2.2. Procedure

2.2.3. Note

2.3. Determining Anesthetic Concentration: Preparation of a Known Standard

2.3.1. Equipment and Reagents

2.3.2. Procedure

2.3.3. Note

3. Behavioral Assays

3.1. Immobility

3.1.1. Equipment and Reagents

3.1.2. Procedure

3.1.3. Note

3.2. Uncoordination

3.2.1. Equipment and Reagents

3.2.2. Procedure

3.2.3. Note

3.3. Radial Dispersion

3.3.1. Equipment and Reagents

3.3.2. Procedure

3.3.3. Notes

3.4. Mating Efficiency

3.4.1. Equipment and Reagents

3.4.2. Procedure

3.5. Body Bends

3.5.1. Equipment and Reagents

3.5.2. Procedure

3.5.3. Note

3.6. Speed of Locomotion

3.6.1. Equipment and Reagents

3.6.2. Procedure

3.7. Anesthetic-Induced Neurotoxicity (Chemotaxis)

3.7.1. Equipment and Reagents

3.7.2. Procedure

3.7.3. Notes

4. Summary and Conclusion

Chapter Eight: Using Drosophila to Understand General Anesthesia: From Synapses to Behavior

1. Multiple Levels of General Anesthetic Action: From Proteins to Circuits to Connectivity

2. Drosophila melanogaster: A Model for Anesthesia Research

3. Behavioral Endpoints: Startle-Induced Locomotion

3.1. Introduction

3.2. Equipment

3.3. Solutions

3.4. Experiment

4. Synaptic Endpoints: Recordings From Individual Boutons

4.1. Introduction

4.2. Equipment

4.3. Solutions

4.4. Dissection.

4.5. Recordings

4.6. Assessing the Quality of Recordings

4.7. Results

5. Conclusion

Chapter Nine: High-Throughput Screening to Identify Anesthetic Ligands Using Xenopus laevis Tadpoles

2. X. laevis Model Organism

3. Ligand Physicochemical Properties and Dose Preparation

4. Behavioral Assessments

5. Screening of Nonvolatile Anesthetics

6. Screening of Volatile Anesthetics

7. Additional Considerations for Novel and/or Chemically Active Ligands

8. Conclusions

Chapter Ten: Zebrafish: A Pharmacogenetic Model for Anesthesia

2. Genetic Manipulation in the Zebrafish

2.1. Reverse Genetics: Recapitulating Human Mutations in Zebrafish

2.2. Expression of Transgenes

2.3. Zebrafish Models of Disorders Linked to Anesthetic Complications

2.4. Forward Genetics: Unbiased Discovery of Genetic Variants That Confer Risk for Anesthesia

3. Behaviors to Assess Sedation and Recovery From Anesthesia

3.1. Photomotor Response (PMR)

3.2. Startle/Vibration Response

4. Anesthesia in Zebrafish

4.1. Types of Anesthetics

4.2. Special Considerations When Making Propofol

4.3. HPLC to Determine Tissue Concentration of Anesthetic

4.4. Propofol Sedation Curve

5. Conclusions

Chapter Eleven: The Mouse as a Model Organism for Assessing Anesthetic Sensitivity

2. Anesthetic Dosing in Mice

2.1. Volatile Anesthetics

2.2. Injectable Anesthetics

3. Determination of Hypnotic Sensitivity in Mice

3.1. Behavioral Testing

3.2. Motor-Independent Measures

4. Assessing Sedation in Mice as a Measure of Anesthetic Sensitivity

4.1. Videographic Analysis of Anesthetic-Induced Reductions in Movement

4.2. Accelerometric Analysis of Anesthetic-Induced Reductions in Movement.

4.3. Electromyographic Analysis of Anesthetic-Induced Reductions in Motor Tone

Section III: Photolabeling

Chapter Twelve: Identification of General Anesthetic Target Protein-Binding Sites by Photoaffinity Labeling and Mass Spec ...

2. Photolabel Design and Synthesis

3. Physicochemical Characterization and Biological Validation

4. Photoaffinity Labeling

5. Mass Spectrometric Analysis

5.1. Sample Preparation

5.1.1. In-Gel Digestion

5.1.2. In-Solution Digestion

5.2. Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)

5.3. Data Analysis

6. Additional Methodologies and Considerations

7. Conclusions

Section IV: Xenon

Chapter Thirteen: Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR

2. X-Ray Crystallography

2.1. Background

2.2. Freeze-Trapping Xe Derivatives

2.2.1. Equipments

2.2.2. Reagents

2.2.3. Procedure

2.2.4. Notes

2.3. Diffraction Data Collection and Analysis

2.3.1. Software

2.3.3. Notes

3. Xe NMR

3.1. Background

3.2. Hyperpolarization

3.3. Hyper-CEST

Further Reading

Chapter Fourteen: Methods for Defining the Neuroprotective Properties of Xenon

2. Biological Action of a Chemically Nonreactive Monoatomic Gas

3. Methods to Explore the Action of Xenon on the N-Methyl-d-Aspartate Subtype of the Glutamate Receptor

4. Methods to Define Which Neuroprotective Indication to Pursue

5. Methods to Define the Neuroprotective Properties of Xenon in Postcardiac Arrest Syndrome

6. Methods to Define That Xenon Protects Against White Matter Brain Injury Following Cardiac Arrest (Hypotheca-Xe NCT0087 ...

7. Methods to Define That Xenon Improves Survival With Good Functional Outcome Following Cardiac Arrest (NCT03176186).

Notes:

Description based on print version record.

ISBN:

9780128127414

0128127414

9780128127407

0128127406