© Jones & Bartlett Learning, LLC.

NOT FOR SALE OR DISTRIBUTION

Biochemistry
for the Pharmaceutical Sciences

Charles P. Woodbury, Jr., PhD

Associate Professor
Department of Medicinal Chemistry
and Pharmacognosy
University of Illinois at Chicago
College of Pharmacy
Chicago, Illinois
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Library of Congress Cataloging-in-Publication Data
Woodbury, Charles P.
Biochemistry for the pharmaceutical sciences / Charles P. Woodbury Jr.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-0-7637-6384-8
ISBN-10: 0-7637-6384-5
1. Biochemistry. 2. Metabolism. 3. Pharmacy. I. Title.
[DNLM: 1. Biochemical Phenomena. 2. Pharmacology—methods. QU 34]
QP514.2.W66 2012
612'.015—dc22
2010047696
6048

Printed in the United States of America

15 14 13 12 11 10 9 8 7 6 5 4 3 2 1
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Contents

Preface xv
Acknowledgments xvii
Reviewers xix

Chapter 1 Biochemical Thermodynamics 1

Basic Quantities and Concepts 1

Terminology 2
First Law: Energy Conservation 3
Second Law: Entropy and the Direction of Spontaneous Change 5
Third Law: An Absolute Scale for Entropies 8
Free Energy Changes 9
Chemical Equilibria 10
Basic Equations 10
Biochemical Standard States 12
Acid–Base Equilibria 12
Coupling of Reactions 13
Reduction–Oxidation Reactions 14
Common Biochemical Conventions 17
Questions for Discussion 18
Reference 19

Chapter 2 Carbohydrates 21

Simple Sugars: Monosaccharides 22

Introduction 22
Basic Nomenclature 22
Stereochemistry 22
Cyclization 25
Reactivity and Common Derivatives 26
Oligosaccharides and Polysaccharides 28
Oligosaccharides 30
Glucose Polymers 31

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iv Contents

Glycosaminoglycans 32
Other Natural Polysaccharides of Interest 35
Biosynthesis of Proteoglycans 36
Other Glycoconjugates 37
Glycolipids 37
Glycoproteins 38
Lectins 39
Clinical Applications 40
Clotting and Heparan/Heparin 40
Blood Group Antigens 40
Blood Glucose Levels, Hemoglobin Glycosylation, and Diabetes 41
Action of Penicillin 41
Questions for Discussion 42
References 42

Chapter 3 Amino Acids and Proteins 45

Amino Acids 46
Roles of Amino Acids 46
General Features of Amino Acids 46
The 20 Common Amino Acids 47
Classification by Properties 52
Some Important but Less Common Amino Acids 53
Polypeptides and Protein Primary Structure 54
Amide Bonds and Peptide Linkages 55
Protein Classification 57
Secondary and Higher-Order Structures 57
Secondary Structure 57
Tertiary Structure 59
Quaternary Structure 63
Flexibility of the Polypeptide Chain 63
Folding of Proteins 66
Protein Unfolding 68
Protein Turnover 69
The Lysosomal System 70
The Ubiquitin/Proteasome System 70
Questions for Discussion 72
References 73

Chapter 4 Nucleic Acids 75

Introduction 76
Major Roles of Nucleotides 77
Bases, Nucleosides, and Nucleotides 78
Primary Structure of DNA and RNA 82
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Contents v

Secondary Structure 83
DNA Secondary Structure 83
RNA Secondary Structure 88
Tertiary and Quaternary Structure 89
Tertiary Structure of tRNA 89
DNA Supercoiling 90
Nucleosomes 94
DNA Denaturation and Renaturation 94
Questions for Discussion 99
References 100

Chapter 5 Lipids and Biomembranes 101

Overview 102
Classes and Biological Roles of Lipids 102
Fat as a Fuel 103
Energy Storage 103
Essential Fatty Acids 105
Chemical Features of Fatty Acids and Acyl Glycerols 105
Nomenclature 105
Other Important Chemical Features of Fatty Acids 108
Triacylglycerols (Triglycerides; Neutral Fats) 109
Phospholipids 110
Major Biological Functions 110
Structure and Nomenclature 111
Cholesterol 113
Biological Roles 113
Structure and Chemical Properties 113
Sphingolipids 114
Biological Roles 114
Structures 115
Eicosanoids 116
Structure and Functions 116
Arachidonic Acid 117
Derivatives of Arachidonic Acid 117
Prostaglandin H Synthase 118
Biomembranes 118
Lipid Bilayers 119
Biomembrane Structure 123
Transport Across Membranes 129
Clinical Applications 131
Cyclo-Oxygenases and Their Inhibition 131
Lipidoses 133
Leukotrienes and Treatments for Asthma 133
Lipopolysaccharides: Endotoxins 134
Questions for Discussion 135
References 136
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vi Contents

Chapter 6 Enzyme Mechanisms and Regulation 139

Introduction 140
General Importance of Enzymes 140
Catalytic Power and Specificity of Enzymes 140
Cofactors in Enzyme Catalysis 141
Active Sites of Enzymes 141
Conformational Change: Induced-Fit Versus
Lock-and-Key Models 143
Enzymatic Catalysis 144
Short Review of Basic Chemical Kinetics Concepts 144
Enzymatic Binding to the Transition State and Rate Acceleration 146
General Mechanisms for Catalysis 147
Classes of Enzymes and Types of Reactions 148
Ribonuclease A: Acid–Base Catalysis 149
Background 149
Substrate Binding: Key Points 150
Mechanism 150
Chymotrypsin and Other Proteases: Covalent Catalysis
and Nucleophiles 152
Background 152
Origins of Substrate Specificity 152
Reaction Mechanism for Chymotrypsin 153
Other Proteases 155
Carbonic Anhydrase: Metal Ions and Electronic Strain 156
Physiological Background 156
Origins of Substrate Specificity 158
Reaction Mechanism 158
Introduction to Cooperativity and Allosterism 160
Allosterism 160
Cooperativity 161
The Concerted or MWC Model of Enzyme Allosterism
and Cooperativity 162
The Sequential or KNF Model 163
Aspartate Transcarbamoylase: An Allosteric Enzyme 164
Background 164
Structure and Conformational Changes 165
Catalytic Mechanism 166
Activation and Inhibition Patterns 166
Regulation by Covalent Modification 167
Reversible Phosphorylation 168
Proteolysis 168
Other Major Types of Covalent Modification 168
Questions for Discussion 169
References 170
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Contents vii

Chapter 7 Models for Enzyme Kinetics 171

Why Study Enzyme Kinetics? 171

The Michaelis-Menten Model 172
A Single Substrate in a Two-Step Reaction Mechanism 172
A Simple Rate Law for this Mechanism 173
Terminology 174
Molecularity and Reaction Order of Enzyme Kinetics 175
Units of Enzyme Activity 176
Numerical Values of Kinetic Parameters 176
Interpretation of the Michaelis Parameter 176
Meaning of kcat/KM 177
Graphical Representations of the Michaelis-Menten Model 178
Determining the Initial Rate of Reaction 178
Direct Plot 179
Double-Reciprocal (Lineweaver-Burk) Plot 180
Reversible Competitive Inhibition 181
General Concepts 181
Mathematics of Competitive Inhibition 182
Graphical Representation for Competitive Inhibition 182
Uncompetitive Inhibition 182
“Mixed” and Noncompetitive Inhibition 183
Active-Site-Directed Irreversible Inhibition 184
Irreversible Inhibition 184
“Suicide Substrates” 185
Heavy Metal Toxicity 186
Nerve Agents 186
Introduction to Design of Enzyme Inhibitors 187
Enzymes as Drug Targets 187
Combination Chemotherapy 187
Examples of Inhibitor Design 187
Questions for Discussion 190
References 193
Appendix 7-1 Derivation of the Michaelis–Menten Equation 193

Chapter 8 Basic Concepts in Metabolism 195

Regulation of Metabolism 196

Feedback in Metabolic Regulation 196
The Crossover Theorem 198
Major Metabolic Control Mechanisms 199
Reciprocal Regulation of Competing Pathways 201
Diet and Nutrition 202
Water 202
Major Food Components 202
Main Pathways for Digestion of Foodstuffs 203
Vitamins and Minerals 204
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viii Contents

Adenosine 5'-Triphosphate 209

ATP Structure 210
Hydrolysis of Phosphoanhydride Bonds 210
Driving an Unfavorable Reaction by Coupling to ATP Hydrolysis 211
The Energy Charge 212
Other “High-Energy” Compounds 213
Basis for the High Free Energy of Hydrolysis 215
Coenzyme A: Carrier of Activated Acyl Groups 215
Structure of Coenzyme A 215
Function 216
Nicotinamides and Flavins: Redox Cofactors 216
Nicotinamides 216
Pellagra and Dietary Deficiency of Niacin 218
Roles of Nicotinamides in the Cell 219
Flavins: FADH2, FMNH2 219
Questions for Discussion 221
References 223

Chapter 9 Major Pathways of Carbohydrate Metabolism 225

Glycolysis 226
Carbohydrate Digestion and Glucose Uptake by Cells 226
Three Stages of the Glycolytic Pathway 227
Energetics of Glycolysis 228
Glycolysis is Anaerobic 229
Other Substrates for Glycolysis 231
Points of Chemical Interest 234
Regulation of Glycolysis 236
Linkage of Glycolysis to Pyruvate Metabolism 237
Central Metabolic Role of Glucose 6-Phosphate 238
Gluconeogenesis 239
The Biosynthetic Pathway to Glucose 239
Net Reaction in Gluconeogenesis 241
Regulation of Gluconeogenesis 241
Feedstocks for Gluconeogenesis 241
The Cori Cycle and Lactate Dehydrogenase 242
Connecting Glycolysis to Gluconeogenesis: The Cori Cycle 242
Role of Lactate Dehydrogenase 242
Aside on Multiple Forms of Enzymes 243
Glycogenolysis and Glycogenesis 246
Structure of Glycogen 246
Glycogen Synthesis 247
Glycogen Breakdown 248
Regulation of Glycogen Metabolism 249
Questions for Discussion 255
References 256
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Contents ix

Chapter 10 Mitochondria and the Citric Acid Cycle 257

Mitochondria 258
Mitochondrial Structure 258
Substrate Transport Systems 259
Pyruvate Dehydrogenase 261
Overview 261
The Pyruvate Dehydrogenase Complex 261
Regulation of the Complex 262
Coenzymes and Prosthetic Groups of the Complex 263
Reaction Scheme for the Pyruvate Dehydrogenase Complex 266
The Citric Acid or Tricarboxylic Acid Cycle 267
General Remarks 267
Regulation 269
Selected Reactions of the TCA Cycle 270
Three-Point Attachment Model 273
Anaplerotic Cycle’s Role in Biosynthesis 274
Requirement for Glucogenic Fuels 276
Aerobic Metabolism and TCA Cycle Function 277
Requirement for Aerobic Conditions 277
Transport of Reducing Equivalents 277
Questions for Discussion 280
References 282

Chapter 11 Respiratory Complexes and ATP Synthesis 283

Respiratory Complexes 284

Overview 284
Flow of Electrons in Respiration 284
Important Coenzymes and Prosthetic Groups 284
Respiratory Complex (Electron Transfer) Proteins
and Their Function 288
Action of ATP Synthase in Oxidative Phosphorylation 293
Structure of ATP Synthase (F0–F1 Complex, Complex V) 293
ATP Synthesis 295
Binding Change Mechanism 296
Proton Electrochemical Free Energy and ATP Synthesis 297
Thermodynamics and ATP Yield 298
Chemiosmotic Coupling 300
Summary of the Chemiosmotic Model 300
Details of the Chemiosmotic Model 300
Clinical Applications 301
Poisons of Respiration 301
Antibiotic Action of Gramicidin A 302
Antibiotic Action of Valinomycin 303
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x Contents

Weight-Reduction Aids 303

Ischemia and ATP Hydrolysis 304
Brown Fat 305
Questions for Discussion 305
References 307

Chapter 12 Other Pathways of Carbohydrate Metabolism 309

Pentose Phosphate Pathway 310

Summary of the Pathway 311
Modes of Operation 311
Glutathione and NADPH 312
Structure and Function of Glutathione 312
Two Important Roles for Glutathione 312
Protection Against Hemolysis 313
Enzyme Deficiency and Malarial Protection 313
Metabolism of Complex Carbohydrates 314
Biosynthesis of Complex Carbohydrates 314
General Synthetic Paths to Complex Carbohydrates 315
Glucuronic Acid and N-Acetylglucosamine 316
Glycoproteins 316
Questions for Discussion 321
References 321

Chapter 13 Lipid Metabolism 323

Uptake and Storage of Lipids 324

Lipid Uptake from the Digestive Tract: Lipoproteins 324
Lipid Transport and Distribution 326
Fatty Acid Storage in Adipocytes 328
Cholesterol Storage 328
Fatty Acid Catabolism 330
Lipolysis and Its Regulation 331
Fate of the Products: Fatty Acids and Glycerol 332
Role of Carnitine 332
b-Oxidation Reaction Sequence 334
Oxidation of Fatty Acids with an Odd Number of Carbons 335
Other Oxidative Systems for Fatty Acids 338
Ketone Bodies and Their Oxidation 340
Ketogenesis 340
Why Ketone Bodies Arise 341
Ketone Body Catabolism 341
Fatty Acid Biosynthesis 344
Reaction Sequence 344
Fatty Acid Synthase Structure and Activities 347
Overall Reaction for Palmitic Acid Synthesis 347
Regulation of Fatty Acid Biosynthesis 348
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Contents xi

Acetyl-CoA Carboxylase 348

Citrate Shuttle 351
Elongation and Modification of Fatty Acids 352
Chain Elongation 352
Desaturation 353
Branched-Chain Fatty Acids 354
Reduction to Fatty Alcohols 354
Triglyceride and Membrane Lipid Biosynthesis 354
Triglyceride Biosynthesis 354
Membrane Lipids from Fatty Acids 355
Cholesterol Metabolism 358
Biosynthesis of Cholesterol 359
Metabolites of Cholesterol 360
Questions for Discussion 363
References 365

Chapter 14 Amino Acid Metabolism 367

Overview of Amino Acid Metabolism 368

Connections with Human Nutrition 369
Digestion of Protein and Amino Acids 369
“Ketogenic” Versus “Glucogenic” 370
Starvation and Fasting 371
Essential Amino Acids 371
Amino Acid Biosynthesis 372
Source of Nitrogen Atoms 372
Six Families for Biosynthesis 373
Details of Biosyntheses in the Serine Family 375
Catabolism of Amino Acids: Transamination and Formation
of a-Keto Acids 378
a-Ketoglutarate Accepts Nitrogens and Glutamate
Releases Ammonia 378
Role of Vitamin B6 379
Mechanism of Transamination 380
Direct Deamination of Serine and Threonine 383
Oxidative Deamination and Ammonia Toxicity 384
Glutamate Dehydrogenase and Oxidative Deamination 384
Ammonia Toxicity 385
Biochemistry and Physiology of Ammonia Transport in the Body 386
Urea Cycle 387
Linkage of Urea Cycle to TCA Cycle 388
Carbamoyl Phosphate 389
Importance of Transmembrane Carriers 389
Regulation of Urea Synthesis 389
Other Biochemical Uses of Ammonia 389
Clinical Applications 390
Phenylalanine Metabolism: Phenylketonuria and Catecholamines 390
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xii Contents

Folate and S-Adenosylmethionine 392

Diseases of Amino Acid Metabolism 398
Drug-Induced Vitamin Deficiencies 399
Hyperammonemia 400
Questions for Discussion 400
References 403

Chapter 15 Nucleotide Metabolism 405

Introduction 405
Purine Biosynthesis 406
Two Major Pathways for Biosynthesis of Nucleotides:
De Novo and Salvage 407
Sources of Purine Skeleton Atoms 407
Ribose Phosphate as a Precursor for Purine Rings 408
Synthesis of Inosine Monophosphate 408
Synthesis of AMP and GMP 411
Feedback Inhibition in Purine Synthesis 411
Pyrimidine Biosynthesis 413
Carbamoyl Phosphate 413
Committed Step 413
Steps to UMP, UTP, and CTP 413
Formation of NTPs and dNTPs 415
Nucleotides with More Phosphates 415
Deoxynucleotides and dTTP Formation 416
Purine and Pyrimidine Breakdown 420
Gout 421
Lesch-Nyhan Syndrome 423
Questions for Discussion 423
References 425

Chapter 16 Synthesis of DNA, RNA, and Proteins 427

Introduction 428
The Central Dogma 428
Bacterial Cell Replication 428
The Eukaryotic Cell Cycle 429
Cyclin-Dependent Kinases 430
Chromosomal Domains and DNA Replication 431
DNA Replication 431
Semiconservative DNA Replication 431
Enzymes of DNA Replication 432
Telomeres 435
Transcription 436
What Is Transcription? 436
Transcription in Prokaryotes 436
Transcription in Eukaryotes 439
Transcript Processing 441
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Contents xiii

Translation 442
Codon Triplets Specify Amino Acids 443
tRNA Carries Activated Amino Acids for Polymerization into
Polypeptide Chains 444
Ribosome Structure 445
Stages in Polypeptide Synthesis 446
Comparing Prokaryotic and Eukaryotic Translation 449
Mutations 451
Different Types of Mutations 451
Mutagens, Mutations, and Repair 452
Defective DNA Repair Can Lead to Cancer or Other Diseases 456
Antimicrobial Agents 457
DNA Polymerase Inhibitors 457
Reverse Transcriptase Inhibitors 458
Topoisomerase Inhibitors 458
RNA Polymerase Inhibitors 458
Ribosome Inhibitors 458
Questions for Discussion 460
References 461

Glossary 463
Index 485
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Preface

This text is based on my course for first-year students in our PharmD curriculum. These
students have taken organic chemistry and are taking physiology concurrently, and they need
to gain a background in enzymology and in primary metabolism for their upcoming courses
in drug therapy. At the University of Illinois at Chicago, we only spend about one semester on
classical biochemical topics. Keeping in mind that we are not preparing students for a career in
biochemical research, we therefore need a shorter, less detailed, and less expensive alternative to
the available large biochemistry textbooks.
This text follows a traditional organization for a course in biochemistry. There are four
main divisions in the text. The first five chapters are largely reviews of topics from organic
and basic physical chemistry; then two chapters on enzymes; then eight chapters on primary
metabolism; and lastly a chapter on topics at the level of molecular biology: DNA replication
and repair, and transcription and translation of genetic messages.
Chapter 1 starts with basic thermodynamic concepts, just enough to help in later explanations
of metabolic strategies.Then comes a series of chapters that introduce (or review) the chemistry
of the fundamental building blocks of biochemistry: carbohydrates, amino acids, nucleic acids,
and lipids. These chapters go from the level of the monomer up to the level of the polymer
(or in the case of the lipids, to the level of the biomembrane). Material at the beginning of
these chapters may be skipped by students who are well-prepared from their organic chemistry
course, though I do recommend that some time be taken with the latter half of each of these
chapters, as the topics here are generally not covered in organic chemistry courses.
Next there are two chapters on enzymology. Chapter 6 is on enzyme mechanisms, while
Chapter 7 deals with mathematical aspects of enzyme kinetics and inhibition. I believe this
approach keeps students interested by making their first contact with enzymology close to
their previous study of reaction mechanisms in organic chemistry. The discussion of enzyme
mechanisms starts with those we can regard as “classical”: ribonuclease A and chymotrypsin. Then
carbonic anhydrase introduces the use of metal ion cofactors; cofactor use is elaborated upon in
later chapters, for example in discussions of the transaminases, of pyruvate dehydrogenase, and
of phenylalanine hydroxylase. Cooperativity and allosterism are introduced via hemoglobin and
aspartate transcarbamoylase.
In the second of these chapters on enzymology, the presentation of the mathematics of
enzyme kinetics is deliberately kept simple, with little derivation of equations (not a useful
exercise for future pharmacists, in my opinion).The Michaelis-Menten model is emphasized, as
is competitive inhibition. There is a very brief introduction to drug design of enzyme inhibitors
as well.

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xvi Preface

The main meat of the text comes after we finish with enzymology. Chapter 8 discusses
the conventions and basic concepts in metabolic biochemistry: pathways, feedback, and other
unifying ideas. Then we move into sugar metabolism and energy generation for the cell
(Chapter 9). Glycolysis is first, then gluconeogenesis and glycogen metabolism. After working
through the tricarboxylic acid cycle and the notion of anaplerosis, we get to respiratory
complexes and the coupling of ATP synthesis in the mitochondrion to proton pumping.
This is followed by a short chapter on the pentose phosphate pathway and the generation of
reducing power for biosynthesis and protection against oxidative agents.
After this, it is time to deal with energy production from lipids; we also need to treat
lipid biosynthesis (Chapter 13). Next comes the metabolism of amino acids (Chapter 14). I have
deliberately emphasized their use as a fuel for the cell over their biosynthesis, to maintain an
emphasis on energy generation for the cell. I wrap up the presentation of primary metabolism
with the synthesis and breakdown of the building blocks of DNA and RNA.
The last chapter is an altogether too brief treatment of cellular transactions with DNA
and RNA. This material is typically the subject of multiple chapters in the large encyclopedic
textbooks of biochemistry, and I have compressed all of this into one chapter. Necessarily I have
left out much; my excuse is that I wished to keep the book to a reasonable length, and my hope
is that most, if not all, of the students using this book will have taken a course in modern cell
biology, where these topics have received their due attention.
The Questions for Discussion at the end of each chapter are intended to spur in-class review
and elaboration of the topics in that chapter. Acquiring the proper specialized vocabulary is
necessary in the study of any scientific subject.Toward this end, I have included a short glossary
of terms used in this text.
Through this organization and approach, and these helpful features, Biochemistry for the
Pharmaceutical Sciences makes this important topic accessible to students.
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Acknowledgments

First, I must acknowledge the support of the Department of Medicinal Chemistry and
Pharmacognosy, University of Illinois at Chicago. I especially appreciate the encouragement
of Dr. Judy Bolton, Head of the Department. I must also thank my colleagues, Dr. Douglas
Thomas and Dr. Joanna Burdette, for their critique of portions of the manuscript.
I also wish to thank the reviewers whose detailed criticisms greatly improved the text.
In preparing several of the figures of proteins and nucleic acids, I have used the Swiss-
PdbViewer (also known as DeepView) to visualize structures from the Protein Data Bank.
Those wishing to learn more about this highly useful program should visit the web site at
http://www.expasy.org/spdbv. The authors of the program have requested that I cite their
publication as well: N. Guex and M.C. Peitsch (1997) Electrophoresis 18:2714–2723.
Finally, I must thank the many students who have patiently pored over my lecture notes
(the precursor to this text), and just as patiently inquired why I had misspelled this, contradicted
myself there, and mis-drew that structure or diagram. Their critiques contributed very
substantially to this book.

xvii
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Reviewers

Cassandra S. Arendt, PhD

Assistant Professor
Pacific University School of Pharmacy

John H. Block, PhD, RPh

Professor Emeritus of Medicinal Chemistry
College of Pharmacy, Oregon State University

Tracey Boncher, PhD

Associate Professor of Medicinal Chemistry/Biochemistry
Ferris State College of Pharmacy

Michael R. Borenstein, RPh, PhD

Associate Dean
Temple University School of Pharmacy

William Chan, PhD

Professor
Thomas J. Long School of Pharmacy and Health Sciences
University of the Pacific

Ganesh Cherala, PhD

Assistant Professor
College of Pharmacy, Oregon State University
Oregon Health & Science University

Gemma P. Geslani, MS, PhD, MPH

Associate Professor of Biochemistry
St. Louis College of Pharmacy

Reza Karimi, RPh, PhD

Assistant Dean for Academic Affairs and Assessment, Associate Professor
Pacific University School of Pharmacy

xix
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xx Reviewers

Evgeny Krynetskiy, PhD, DSc

Associate Professor
Temple University School of Pharmacy

John C. Matthews, PhD

Professor of Pharmacology
University of Mississippi School of Pharmacy

Sigrid C. Roberts, PhD

Assistant Professor
Pacific University School of Pharmacy