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A Pharmacology Primer

Techniques for More Effective and

Strategic Drug Discovery

FIFTH EDITION

Terry P. Kenakin, PhD

Professor, Department of Pharmacology, University of North Carolina
School of Medicine, United States
Table of Contents

Title page

Copyright

Dedication

Preface

Chapter 1. What is Pharmacology?

Abstract

1.1 About This Book

1.2 What is Pharmacology?

1.3 The Receptor Concept

1.4 Pharmacological Test Systems

1.5 The Nature of Drug Receptors

1.6 Pharmacological Intervention and the Therapeutic

Landscape

1.7 System-Independent Drug Parameters: Affinity and Efficacy

1.8 What is Affinity?

 1.9 The Langmuir Adsorption Isotherm

1.10 What is Efficacy?

1.11 Dose–Response Curves

1.12 Chapter Summary and Conclusions

1.13 Derivations: Conformational Selection as a Mechanism of

Efficacy

References

Chapter 2. How Different Tissues Process Drug Response

Abstract

2.1 Drug Response as Seen Through the “Cellular Veil”

2.2 The Biochemical Nature of Stimulus–Response Cascades

2.3 The Mathematical Approximation of Stimulus–Response

Mechanisms

2.4 Influence of Stimulus–Response Cascades on Dose–

Response Curve Slopes

2.5 System Effects on Agonist Response: Full and Partial

Agonists

2.6 Differential Cellular Response to Receptor Stimulus

2.7 Receptor Desensitization and Tachyphylaxis

2.8 The Measurement of Drug Activity

2.9 Advantages and Disadvantages of Different Assay Formats

 2.10 Drug Concentration as an Independent Variable

2.11 Chapter Summary and Conclusions

2.12 Derivations

References

Further Reading

Chapter 3. Drug–Receptor Theory

Abstract

3.1 About This Chapter

3.2 Drug–Receptor Theory

3.3 The Use of Mathematical Models in Pharmacology

3.4 Some Specific Uses of Models in Pharmacology

3.5 Classical Model of Receptor Function

3.6 The Operational Model of Receptor Function

3.7 Two-State Theory

3.8 The Ternary Complex Model

3.9 The Extended Ternary Complex Model

3.10 Constitutive Receptor Activity and Inverse Agonism

3.11 The Cubic Ternary Complex Model

3.12 Multistate Receptor Models and Probabilistic Theory

 3.13 Chapter Summary and Conclusions

3.14 Derivations

References

Chapter 4. Pharmacological Assay Formats: Binding

Abstract

4.1 The Structure of This Chapter

4.2 Binding Theory and Experiment

4.3 Complex Binding Phenomena: Agonist Affinity from Binding

Curves

4.4 Experimental Prerequisites for Correct Application of Binding

Techniques

4.5 Binding in Allosteric Systems

4.6 Chapter Summary and Conclusions

4.7 Derivations

References

Chapter 5. Agonists: The Measurement of Affinity and Efficacy in

Functional Assays

Abstract

5.1 Functional Pharmacological Experiments

5.2 The Choice of Functional Assays

 5.3 Recombinant Functional Systems

5.4 Functional Experiments: Dissimulation in Time

5.5 Experiments in Real Time Versus Stop-Time

5.6 Quantifying Agonism: The Black–Leff Operational Model of

Agonism

5.7 Biased Signaling

5.8 Null Analyses of Agonism

5.9 Comparing Full and Partial Agonist Activities: Log(max/EC50)

5.10 Chapter Summary and Conclusions

5.11 Derivations

References

Chapter 6. Orthosteric Drug Antagonism

Abstract

6.1 Introduction

6.2 Kinetics of Drug–Receptor Interaction

6.3 Surmountable Competitive Antagonism

6.4 Noncompetitive Antagonism

6.5 Agonist–Antagonist Hemiequilibria

6.6 Resultant Analysis

6.7 Antagonist Receptor Coverage: Kinetics of Dissociation

 6.8 Blockade of Indirectly Acting Agonists

6.9 Irreversible Antagonism

6.10 Chemical Antagonism

6.11 Chapter Summary and Conclusions

6.12 Derivations

References

Chapter 7. Allosteric Modulation

Abstract

7.1 Introduction

7.2 The Nature of Receptor Allosterism

7.3 Unique Effects of Allosteric Modulators

7.4 Functional Study of Allosteric Modulators

7.5 Methods for Detecting Allosterism

7.6 Chapter Summary and Conclusions

7.7 Derivations

References

Chapter 8. The Optimal Design of Pharmacological Experiments

Abstract

8.1 Introduction
 8.2 The Optimal Design of Pharmacological Experiments

8.3 Null Experiments and Fitting Data to Models

8.4 Interpretation of Experimental Data

8.5 Predicting Therapeutic Activity in All Systems

8.6 Summary and Conclusions

8.7 Derivations

References

Further Reading

Chapter 9. Pharmacokinetics

Abstract

9.1 Introduction

9.2 Biopharmaceutics

9.3 The Chemistry of “Druglike” Character

9.4 Pharmacokinetics

9.5 Nonlinear Pharmacokinetics

9.6 Multiple Dosing

9.7 Modifying Pharmacokinetics Through Medicinal Chemistry

9.8 Practical Pharmacokinetics

9.9 Placement of Pharmacokinetic Assays in Discovery and

Development
 9.10 Summary and Conclusions

References

Chapter 10. Safety Pharmacology

Abstract

10.1 Safety Pharmacology

10.2 Hepatotoxicity

10.3 Cytotoxicity

10.4 Mutagenicity

10.5 hERG Activity and Torsades De Pointes

10.6 Autonomic Receptor Profiling and Off-Target Effects

10.7 General Pharmacology

10.8 Clinical Testing and Drug Toxicity

10.9 Summary and Conclusions

References

Chapter 11. The Drug Discovery Process

Abstract

11.1 Some Challenges for Modern Drug Discovery

11.2 Target-Based Drug Discovery

11.3 Systems-Based Drug Discovery

 11.4 In Vivo Systems, Biomarkers, and Clinical Feedback

11.5 Types of Therapeutically Active Ligands: Polypharmacology

11.6 Pharmacology in Drug Discovery

11.7 Chemical Sources for Potential Drugs

11.8 Pharmacodynamics and High-Throughput Screening

11.9 Clinical Testing

11.10 Summary and Conclusions

References

Chapter 12. Statistics and Experimental Design

Abstract

12.1 Structure of This Chapter

12.2 Introduction

12.3 Descriptive Statistics: Comparing Sample Data

12.4 How Consistent is Experimental Data with Models?

12.5 Comparison of Samples to “Standard Values”

12.6 Experimental Design and Quality Control

12.7 Chapter Summary and Conclusions

References

Chapter 13. Selected Pharmacological Methods

 Abstract

13.1 Binding Experiments

13.2 Functional Assays

Reference

Chapter 14. Exercises in Pharmacodynamics and Pharmacokinetics

Abstract

14.1 Introduction

14.2 Agonism

14.3 Antagonism

14.4 In Vitro–In Vivo Transitions and General Discovery

14.5 SAR Exercises

14.6 Pharmacokinetics

14.7 Conclusions

References

Index
Copyright
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Dedication

As always … for Debbie

Preface
Terry Kenakin, Research Triangle Park
Science is an evolving process, so books on science should routinely
be expected to evolve from being “out of date” to “needing to be
updated.” From that standpoint alone, a book such as “A
Pharmacology Primer” should be brought up to date every so often.
But in this particular case, there are unique reasons why “A
Pharmacology Primer” should be updated. This book describes the
role of pharmacology in drug discovery and also that pharmacology
is a unique discipline made up of an amalgam of biological and
chemical disciplines. Therefore, any advancement in any one of
those component disciplines impacts pharmacology and emerges as
its modification; the result is a constantly changing landscape of
possibilities. In this most recent edition, the advances in structural
protein chemistry and increased understanding of cellular signaling
has changed the landscape of discovery and the way
pharmacologists approach research challenges. Specifically, the “null
method” approaches used in the past, necessary because of the lack
of knowledge of the cellular processes that drugs modify, are giving
way to detailed mechanistic models of what actually is going on in
pharmacological systems on a molecular level. This makes
comparison of the verisimilitude of pharmacological data to models,
in the process of determining predictive parameters of drug activity,
a more facile process with the potential to attack the presently most
important reason for new drug candidate failure, namely, lack of
therapeutic efficacy. There are at least two reasons for the high (50%)
rate of candidate failure; one may be with us for some time, namely,
the lack of understanding of exactly what it is we need to do to
correct faulty physiology in disease. However, we may be able to
impact the second reason by doing a better job of determining the
true pharmacological efficacies of the molecules we advance to the
clinic and to better translate the clinical results with pharmacological
profiles. This text is part of the application of new pharmacological
data toward that endpoint.
2018
CHAPTER 1
What is Pharmacology?
Abstract
In this chapter, the relevance of pharmacology to new drug
discovery is presented as well as the two most important
properties of drugs used to quantify drug activity; affinity and
efficacy. The groundwork for the rest of the volume is completed
with discussions of the receptor concepts, different biological
drug targets and the major tool used in pharmacological
experimentation (dose–response curves).

Keywords
Pharmacology; drug receptors; affinity; efficacy and dose–response
curves

I would in particular draw the attention to physiologists to this type of

physiological analysis of organic systems which can be done with the
aid of toxic agents ….

—Claude Bernard (1813–78).

OUTLINE

1.1 About This Book 1

1.2 What is Pharmacology? 1
1.3 The Receptor Concept 3
1.4 Pharmacological Test Systems 4
1.5 The Nature of Drug Receptors 7
1.6 Pharmacological Intervention and the Therapeutic
Landscape 7
1.7 System-Independent Drug Parameters: Affinity and
Efficacy 10
1.8 What is Affinity? 13
1.9 The Langmuir Adsorption Isotherm 13
1.10 What is Efficacy? 15
1.11 Dose–Response Curves 16
1.12 Chapter Summary and Conclusions 19
1.13 Derivations: Conformational Selection as a Mechanism of
Efficacy 20
References 21
1.1 About This Book
Essentially this is a book about the methods and tools used in
pharmacology to quantify drug activity. Receptor pharmacology is
based on the comparison of experimental data and simple
mathematical models, with a resulting inference of drug behavior to
the molecular properties of drugs. From this standpoint, a certain
level of understanding of the mathematics involved in the models is
useful but not imperative. This book is structured such that each
chapter begins with the basic concepts and then moves on to the
techniques used to estimate drug parameters, and, finally, for those
so inclined, the mathematical derivations of the models used.
Understanding the derivation is not a prerequisite for understanding
the application of the methods or the resulting conclusion; these are
included for completeness and are for readers who wish to pursue
exploration of the models. In general, facility with mathematical
equations is definitely not required for pharmacology; the derivations
can be ignored without any detriment to the use of this book.
Second, the symbols used in the models and derivations, on
occasion, duplicate each other (i.e., α is an extremely popular
symbol). However, the use of these multiple symbols has been
retained, since this preserves the context of where these models were
first described and utilized. Also, changing these to make them
unique would cause confusion if these methods were to be used
beyond the framework of this book. Therefore, care should be taken
to consider the actual nomenclature of each chapter.
Third, an effort has been made to minimize the need to cross-
reference different parts of the book (i.e., when a particular model is
described, the basics are reiterated somewhat to minimize the need to
read the relevant but different part of the book in which the model is
initially described). While this leads to a small amount of repeated
description, it is felt that this will allow for a more uninterrupted flow
of reading and use of the book.
1.2 What is Pharmacology?
Pharmacology (an amalgam of the Greek pharmakos, medicine or drug,
and logos, study) is a broad discipline describing the use of chemicals
to treat and cure diseases. The Latin term pharmacologia was used in
the late 1600s, but the term pharmacum was used as early as the fourth
century to denote the term drug or medicine. There are subdisciplines
within pharmacology representing specialty areas. Pharmacokinetics
deals with the disposition of drugs in the human body. To be useful,
drugs must be absorbed and transported to their site of therapeutic
action. Drugs will be ineffective in therapy if they do not reach the
organs(s) to exert their activity; this will be discussed specifically in
Chapter 9, Pharmacokinetics, of this book. Pharmaceutics is the study
of the chemical formulation of drugs to optimize absorption and
distribution within the body. Pharmacognosy is the study of plant
natural products and their use in the treatment of disease. A very
important discipline in the drug-discovery process is medicinal
chemistry, the study of the production of molecules for therapeutic
use. This couples synthetic organic chemistry with an understanding
of how biological information can be quantified and used to guide the
synthetic chemistry to enhance therapeutic activity. Pharmacodynamics
is the study of the interaction of the drug molecule with the biological
target (referred to generically as the “receptor,” vide infra). This
discipline lays the foundation of pharmacology since all therapeutic
application of drugs has a common root in pharmacodynamics (i.e.,
as a prerequisite to exerting an effect, all drug molecules must bind to
and interact with receptors).
The history of pharmacology is tied to the history of drug
discovery—see Chapter 8, The Optimal Design of Pharmacological
Experiments. As put by the great Canadian physician Sir William
Osler (1849–1919; the “father of modern medicine”), “… the desire to
take medicine is perhaps the greatest feature which distinguishes
man from animals ….” Pharmacology as a separate science is
approximately 120–140 years old. The relationship between chemical
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