xx

1. 1 3Reference
Methodology, Concepts,
and Mode-of-Action
Drug Design
Gerhard Klebe

2. Drug Design

4. Gerhard Klebe
Drug Design
Methodology, Concepts, and
Mode-of-Action
With 494 Figures and 44 Tables

5. Gerhard Klebe
Institute of Pharmaceutical Chemistry
Philipps-University Marburg
Marburg, Germany
Translator
Leila Telan
D€
usseldorf, Germany
ISBN 978-3-642-17906-8 ISBN 978-3-642-17907-5 (eBook)
ISBN 978-3-642-17908-2 (print and electronic bundle)
DOI 10.1007/978-3-642-17907-5
Springer Heidelberg New York Dordrecht London
This work is based on the second edition of “Wirkstoffdesign”, by Gerhard Klebe, published
by Spektrum Akademischer Verlag 2009, ISBN: 978-3-8274-2046-6
Library of Congress Control Number: 2013933987
# Springer-Verlag Berlin Heidelberg 2013
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6. Preface
The present handbook on drug design builds on the German version first written by
Hans-Joachim Böhm, Hugo Kubinyi, and me in 1996. After 12 years of success on
the market, the German version of this handbook was entirely rewritten and
significantly extended, then by me as the sole author. The new edition particularly
considers novel approaches in drug discovery and many successful examples
reported in literature on structure-based drug design and mode-of-action analysis.
This novel version appeared in 2009 on the German market. Several attempts were
made to translate this book into English to make it available to a wider audience.
This intention was driven by the fact that the author was repeatedly approached
with the question as to why such a successful book is not available in the English
language. An analysis of the textbook market made apparent that no similar
compendium was (and still is) available covering the same field of interest. Finally,
Springer agreed in the translation project, and Dr. Leila Telan, a gifted bilingual
medicinal chemist and physician, was found willing to take the task of producing
a first draft of a cover-to-cover translation of the German original. This version was
corrected, and some chapters extended by the author. The book is meant for
students of chemistry, pharmacy, biochemistry, biology, chemical biology, and
medicine interested in the design of new active agents and the structural founda-
tions of drug action. But it is also tailored to experts in drug industry who want to
obtain a more comprehensive overview of various aspects of the drug discovery
process.
Such a book project would not have been possible without the help of many
friends and colleagues. First of all, I want to express my sincere thanks to Dr. Leila
Telan, D€
usseldorf, Germany, who produced the first version of this translation. Her
version and the modifications of the author have been carefully proofread by many
colleagues in the field. Their help is highly appreciated. Furthermore, I would like
to acknowledge the help of Prof. Dr. Hugo Kubinyi, Heidelberg, Germany, who
assisted in correcting the first version of the English translation. Particular thanks
go to Dr. Simon Cottrell, Cambridge, England, and to Dr. Nathan Kilah, Hobat,
Tasmania, Australia, for their excellent and very thorough proofreading of the
different chapters. The project was ideally guided by Dr. Daniel Quinones and
v

7. Dr. Sylvia Blago, Springer, Heidelberg, Germany. The author is grateful to the
publisher for their assistance and technical support in producing the electronic and
printed version of this handbook.
Marburg, Germany, May 2013 Gerhard Klebe
vi Preface

8. Contents
Part I Fundamentals in Drug Research . . . . . . . . . . . . . . . . . . . . . . 1
1 Drug Research: Yesterday, Today, and Tomorrow . . . . . . . . . . . . 3
2 In the Beginning, There Was Serendipity . . . . . . . . . . . . . . . . . . . 23
3 Classical Drug Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4 Protein–Ligand Interactions as the Basis for Drug Action . . . . . . 61
5 Optical Activity and Biological Effect . . . . . . . . . . . . . . . . . . . . . . 89
Part II The Search for the Lead Structure . . . . . . . . . . . . . . . . . . . 111
6 The Classical Search for Lead Structures . . . . . . . . . . . . . . . . . . . 113
7 Screening Technologies for Lead Structure Discovery . . . . . . . . . 129
8 Optimization of Lead Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 153
9 Designing Prodrugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
10 Peptidomimetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Part III Experimental and Theoretical Methods . . . . . . . . . . . . . . . 209
11 Combinatorics: Chemistry with Big Numbers . . . . . . . . . . . . . . . . 211
12 Gene Technology in Drug Research . . . . . . . . . . . . . . . . . . . . . . . . 233
13 Experimental Methods of Structure Determination . . . . . . . . . . . 265
14 Three-Dimensional Structure of Biomolecules . . . . . . . . . . . . . . . 291
15 Molecular Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
16 Conformational Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
vii

9. Part IV Structure–Activity Relationships and Design
Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
17 Pharmacophore Hypotheses and Molecular Comparisons . . . . . . 349
18 Quantitative Structure–Activity Relationships . . . . . . . . . . . . . . . 371
19 From In Vitro to In Vivo: Optimization of ADME and
Toxicology Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
20 Protein Modeling and Structure-Based Drug Design . . . . . . . . . . 429
21 A Case Study: Structure-Based Inhibitor Design for
tRNA-Guanine Transglycosylase . . . . . . . . . . . . . . . . . . . . . . . . . . 449
Part V Drugs and Drug Action: Successes of Structure-Based
Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
22 How Drugs Act: Concepts for Therapy . . . . . . . . . . . . . . . . . . . . . 471
23 Inhibitors of Hydrolases with an Acyl–Enzyme Intermediate . . . . 493
24 Aspartic Protease Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
25 Inhibitors of Hydrolyzing Metalloenzymes . . . . . . . . . . . . . . . . . . 565
26 Transferase Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 599
27 Oxidoreductase Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641
28 Agonists and Antagonists of Nuclear Receptors . . . . . . . . . . . . . . 697
29 Agonists and Antagonists of Membrane-Bound Receptors . . . . . . 719
30 Ligands for Channels, Pores, and Transporters . . . . . . . . . . . . . . 745
31 Ligands for Surface Receptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 777
32 Biologicals: Peptides, Proteins, Nucleotides, and Macrolides
as Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 813
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851
Illustration Source References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 853
Name Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 863
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 867
viii Contents

10. Introduction
Drug design is a science, a technology, and an art all in one. An invention is the
result of a creative act, and a discovery is the detection of an already-existing
reality. Design encompasses the two processes with emphasis on a targeted
approach based on the available knowledge and technology. Furthermore, the
creativity and intuition of the researcher play a decisive role.
Drugs are all substances that affect a system by inducing a particular effect. In
the context of this book, drugs are substances that exhibit a biochemical or
pharmacological effect, in most cases medications, that achieve a therapeutic result
in humans.
The idea of rational drug design is not new. Organic compounds were prepared
more than a century ago with the goal of attaining new medicines. The sedatives
chloral hydrate (1869) and urethane (1885), and the antipyretics phenacetin
(1888) and acetylsalicylic acid (1897) are early examples of how targeted com-
pounds can be made that have favorable therapeutic properties by starting with
a working hypothesis. The fact, that the hypotheses in all four cases were more or
less incorrect (▶ Sects. 2.1, ▶ 2.2, and ▶ 3.1) simultaneously demonstrates one of
the main problems of drug design.
In the case of the artistic design of a poster or commodity, or, in the case of
engineering, the design of an automobile, a computer, or a machine, the result is
usually predictable. In contrast, the design of a drug is even today not completely
foreseeable. The consequences of the smallest structural changes of a drug on its
biological properties and target tissue are too multifaceted and at present too poorly
understood.
Until modern times, scientists have worked on the principle of trial and error to
find new medicines. By this they derived mostly empirical rules that have contrib-
uted to a knowledge base for rational drug design and which has been translated by
individual researchers more or less successfully into practice. Today new technol-
ogies are available for drug research, for instance, combinatorial chemistry, gene
technology, and automated screening methods with high throughput, protein crys-
tallography and fragment screening, virtual screening, and the application of bio-
and chemoinformatics.
ix

11. In many cases the molecular mechanisms of the mode of action of medicines are
fairly well understood, but in other cases we are at the threshold of comprehension.
Many of these mechanisms will be discussed in this book. Progress in protein
crystallography and NMR spectroscopy allows the determination of the three-
dimensional structure of protein–ligand complexes on a routine basis. As is
shown in many of the illustrations in this book (for a general explanation of
“reading” these illustrations, see the appendix at the end of this book) these
structures make a decisive contribution to the targeted design of drugs. 3D struc-
tures with up to atomic resolution are known for approximately 550,000 small
molecules and more than 85,000 proteins and protein–ligand complexes, and the
numbers are increasing exponentially. Methods for the prediction of the 3D struc-
tures of small molecules are now mature, and semiempirical and ab initio quantum
chemical calculations on drugs are now routinely performed. The sequencing of the
human genome is complete, and the genomes of other organisms are reported nearly
every week, including those of important human pathogens. The age of structural
genomics has begun, and it is only a matter of time before the 3D structures of entire
gene families are available. Given enough sequence homology, modeling programs
can nowadays achieve an impressive reliability. In the meantime, the composition of
entire genomes is being processed with structure-prediction programs. There are
already interesting approaches for the de novo prediction of 3D protein structures,
and the first correct 3D structural predictions have been successfully accomplished.
Structure-based and computer-aided design of new drugs is here to stay in
practical drug research. Computer programs serve the search for, modeling of,
and targeted design of new drugs. In countless cases these techniques have assisted
the discovery and optimization of new drugs. On the other hand, a too-strict and
one-sided focus on the computational results bears the danger of losing sight of the
available knowledge of the relationship between the chemical structure and bio-
logical activity. Another danger is the limited consideration of an active agent only
with respect to its interaction with one single target without considering the other
essential requirements for a drug, for instance, the pharmacokinetic and toxicolog-
ical properties. In the last decade, intensive research effort has gone into the
compilation of empirical guidelines to predict bioavailability, toxicological pro-
files, and metabolic properties (ADME parameters). The ability to predict the
metabolic profile for a given xenobiotic by the arsenal of cytochrome P450
enzymes or to predict for each individual patient the metabolic peculiarities is
still a dream. Nonetheless, just such an individually adjusted therapy and dosing
regime is within the realm of possibilities. It is also conceivable that in the
foreseeable future, gene sequencing of each of us will be financially feasible and
will require a manageable and justifiable amount of time and effort. This will open
entirely new perspectives for drug research. Whether this pushes open the gate to
individualized personal medicines will be a question of cost. The theme of this book
is to introduce the methods required for drug design particularly based on structural
and mechanistic evidence. By the use of well-selected examples the route to the
discovery and development of new medicines is discussed and will be reflected
under the constantly changing conditions.
x Introduction

12. Drug research is a multidisciplinary field in which chemists, pharmacists,
technologists, molecular biologists, biochemists, pharmacologists, toxicologists,
and clinicians work together to pave the way for a substance to become
a therapeutic. Because of this, the majority of drug developments is done in an
industrial setting. It is only there that the financial requirements and structural
organization are in place to allow a successful cooperation of all disciplines that are
necessary to channel the research in the required manner toward a common goal.
The fundamentals and future-oriented innovations of drug research are, however,
increasingly being established in academia. Interestingly, an increasing amount of
research activities at the universities have recently been devoted to drug develop-
ments for infectious diseases and for diseases that particularly afflict developing
countries, which have been sorely neglected by the profit oriented pharmaceutical
industry of the industrialized world. This is even more alarming when we consider
that our improved quality of life and prolonged life expectancy are attributable to,
above all else, a victory over devastating infectious diseases. We can only hope
that politicians recognize this situation in time and make the resources and
organizational infrastructure available so that the academic research groups can
step into the breach in an efficient and goal-oriented way.
The rising costs of research and development, an already high standard of health
care in many indications, and distinctly increased safety awareness and the con-
comitant demanding standards of the regulatory authorities have caused the number
of new chemical entities (NCE) to steadily decrease over the last decades from 70–
100 per year from 1960 to 1969, to 60–70 from 1970 to 1979, to an average of 50
between 1980 and 1989, to 40–45 in the 1990s, and even less in the new millen-
nium. Despite this, there have still been new developments, and distinct progress
has been made in the therapy of, for example, psychiatric diseases, arterial hyper-
tension, gastrointestinal ulcers, and leukemia in addition to the broadening of
indications for older compounds. Of the blockbusters, a disproportionately large
percentage of the drugs were found in the last years by using a rational approach.
The cost of developing and launching a new drug has increased continuously; to
date, it is between US $800–$1,600 million. Only large pharmaceutical companies
can still afford these costs, with the associated risk of failure in the last phases of
clinical trials, or a misjudgment of the therapeutic potential of a new drug.
There is talk nowadays of a paradigm shift in pharmaceutical research. In
research this refers to the use of new technologies; in the market place this refers
to a concentration process of corporate mergers and acquisitions. The last decade
brought about many such “mega-mergers.” Larger and larger sales figures are being
achieved by fewer and fewer companies. In parallel to this, a very dynamic and
hardly insignificant scene has developed of small- to medium-sized, highly flexible
biotech companies. The areas of gene technology, combinatorial chemistry, sub-
stance profiling, and rational design are particularly well represented in numerous
such companies. Larger companies try to outsource their riskier research concepts
to these companies and contract their services for everything up to the development
of clinical candidates. However, the success of this scene has led to the result that
the “good” companies have been swallowed by the “big” companies. Many former
Introduction xi

13. employees of “big pharma” have established their own small companies with an
innovative idea. If the idea was good and successful, after a few years these
innovators find themselves once again incorporated into the organization of
a “big pharma” company.
At the same time the prescribing practices in all areas of health care have
changed. Formerly it was the physician alone, occasionally in consultation with
a pharmacist, who was responsible for the pharmacological therapy of the patient.
Today cost-cutting measures, “negatives lists,” health insurance, the purchasing
departments of hospitals and pharmacies, the ubiquitous Internet, and even public
opinion influence therapies to an ever larger extent.
The drug market, with its US $600 billion, is an extremely attractive market.
Furthermore, this market is characterized by dynamic growth, which is decidedly
more than in other markets. The best selling drug in 2005, Lipitor®
(Sortis®
in
Europe; atorvastatin) achieved US $12.2 billion in annual sales. Only illegal
narcotics like heroin and cocaine have higher sales figures.
Tailored medications – Will the latest technologies really deliver on this prom-
ise? What makes drug research so difficult? To use a parable, it is something like
playing against an almighty chess computer. The rules are known to both sides, but
it is very difficult to comprehend the consequences of each individual move during
a complicated middle game. A biological organism is an extremely complicated
system. The effect of a drug on the system and the effect of the system on the drug
are multifaceted. Every structural change made with the goal of optimizing one
particular characteristic simultaneously changes the finely tuned equilibrium of the
other characteristics of the drug.
The knowledge of the interplay between the chemical structure and the biolog-
ical effect must be united with the newest technology and results of genetic research
to purposefully develop new medicines. It is also necessary to define the range of
applications and the limitations of new technologies. Theory and modeling cannot
exist detached from experiment. The results of calculations depend strongly on the
boundary parameters of the simulation. The results collected at one system are only
conditionally transferable to other systems. Only an experienced specialist is in
a position to fully exploit the special potential of theoretical approaches. The claims
that some software and venture capital companies make, that their results automat-
ically lead to success, should be considered with some skepticism. This book should
be helpful in these situations too, to separate the wheat from the chaff and to
identifying the application range of these method as well as their limitations.
This book is about drug research and the mode of action of medicines. It is
different from classical textbooks on pharmaceutical chemistry in its structure and
goals. The principles, methods, and problems associated with the search for new
medicines are the themes. Classes of drugs are not discussed, but rather the way that
these drugs were discovered and some insights into the structural requirements for
their action on a particular target protein. As the title suggests, the book is meant for
students of chemistry, pharmacy, biochemistry, biology, and medicine who are
interested in the art of designing new medicines and the structural fundamentals of
how drugs act on their targets.
xii Introduction

14. In the first section, after an introduction to the history of medicines and the
concept of serendipity as an unpredictable but always very successful concept in
drug research, examples from classical drug research will be presented.
A discussion about the fundamentals of drug action, the ligand–receptor interaction,
and the influence of the three-dimensional structure on the efficacy of a drug round
the section out. In the second section, the search for lead structures and their
optimization and the use of prodrug strategies are introduced. New screening
technologies but also the systematic modification of structures by using the concept
of bioisosteres and a peptidomimetic approach are discussed. In the third section,
experimental and theoretical methods applied in drug research are described.
Combinatorial chemistry has afforded access to a wide variety of test substances.
Gene technology has produced the target proteins in their pure form, and has helped
to characterize these proteins’ properties and function from the molecular level to
the cellular assembly, all the way to the organism level. It has built a bridge between
understanding the effects of a drug therapy on the complex microstructure of a cell
and in systems biology of an organism. The spatial structure of proteins and
protein–ligand complexes are accessible through NMR spectroscopy and X-ray
crystallography. Their structural principles are becoming better understood and are
increasingly allowing us access to the binding geometry of the drugs. The computer
methods and molecular dynamics simulations of complex conformational analysis
have also sharpened our understanding of targeted drug design. The fourth section
introduces design techniques such as pharmacophore and receptor modeling, and
discusses the methods of, and uses for, quantitative structure–activity relationships
(QSAR). Insights into the transport and distribution of drugs in biological systems
are given, and different techniques for structure-based design are presented. A drug-
design case study from the author’s research closes the chapter. The fifth section of
this book focuses on the core question of pharmacology: How drugs actually work?
Enzymes, receptors, channels, transporters, and surface proteins are divided into
individual chapters and discussed as a group of target proteins. The spatial structure
of the protein and modes of action are used to elucidate in detail why a drug works
and why it must exhibit a particular geometry and structure to work. Exemplarily,
the contributions of structure-based and computer-aided design to the discovery of
new drugs are presented in these chapters, and other aspects are also shifted into the
spotlight.
Because of the concept of this book, many important drugs are not considered or
are only fleetingly mentioned. The same is true of receptor theory, pharmacokinet-
ics and metabolism, the basics of gene technology, and statistical methods. The
biochemical, molecular biological, and pharmacological fundamentals of the mode
of action of drugs, which are important for the understanding of the theme of drug
design, are only commented upon in outline form. Other disciplines that are critical
for the development of an active substance to a medicine and application to
patients, such as pharmaceutical formulations, toxicological testing, and clinical
trials, are not themes that are covered in this book.
The selection of examples from therapeutic areas was made subjectively and for
didactic reasons based on case studies and to bring other aspects of drug research to
Introduction xiii

15. the foreground. A balanced presentation of the methods of drug design and their
practical application was attempted. The interested reader does not have to read the
book chronologically. If the reader’s interest is purely on drugs and their mode of
action, then they can also begin with ▶ Chap. 22. There are many cross references
in the text to help the reader to find the passages in other parts of the book that are
necessary for an exact comprehension of what is being discussed at any given part.
The references and literature suggestions that follow cite particularly recommend-
able monographs and are ordered alphabetically; journals and series on the themes
that are discussed in later chapters are not mentioned specifically again.
Literature
Monographs
Brunton L, Lazo J, Parker K (2005) Goodman & Gilman’s the pharmacological basis of thera-
peutics, 11th edn. McGraw-Hill, Europe
Ganellin CR, Roberts SM (eds) (1993) Medicinal chemistry. The role of organic chemistry in drug
research, 2nd edn. Academic Press, London
King FD (ed) (2003) Medicinal chemistry: principles and practice, 2nd edn. The Royal Society of
Chemistry, Cambridge
Krogsgaard-Larsen P, Bundgaard H (eds) (1991) A textbook of drug design and development.
Harwood Academic Publishers, Chur, Schweiz
Lednicer D (ed) (1993) Chronicles of drug discovery, vol 3. American Chemical Society,
Washington, DC and earlier volumes from this series
Lemke TL, Williams DA (2008) Foye’s principles of medicinal chemistry, 6th edn. Williams &
Wilkins, Baltimore
Mannhold R, Kubinyi H, Folkers G (eds) Methods and principles in medicinal chemistry. Wiley-
VCH, Weinheim, Series with Guest Editors
Maxwell RA, Eckhardt SB (1990) Drug discovery. A casebook and analysis. Humana Press,
Clifton
Mutschler E, Derendorf H (1995) Drug action, basic principles and therapeutic aspects. CRC
Press:Boca Raton/Ann Arbor/London/Tokyo
Silverman RB (2004) The organic chemistry of drug design and drug action, 2nd edn. Elsevier/
Academic Press, Burlington
Wermuth CG, Koga N, König H, Metcalf BW (eds) (1992) Medicinal chemistry for the 21st
century. Blackwell Scientific, Oxford
Journals and Series
Annual Reports in Medicinal Chemistry
Chemistry & Biology
ChemMedChem
Drug Discovery Today
Drug News and Perspectives
Journal of Computer-Aided Molecular Design
Journal of Medicinal Chemistry
Methods and Principles in Medicinal Chemistry
xiv Introduction

16. Nature
Nature Reviews Drug Discovery
Perspectives in Drug Discovery and Design
Pharmacochemistry Library
Progress in Drug Research
Quantitative Structure-Activity Relationships
Reviews in Computational Chemistry
Science
Scientific American
Trends in Pharmacological Sciences
Nowadays the Internet, discussion platforms, and the tremendously valuable tool of Wikipedia are
available to everyone and provide access to an enormous source of information.
Introduction xv

18. Part I
Fundamentals in Drug Research

19. This colored copper plate engraving from arguably the most beautiful plant book,
the Hortus Eystettensis by Basilius Besler, Eichst€
att, 1613, shows the squill, Scilla
alba (modern name: Urginea maritima L.). This plant was known to the ancient
Egyptians, Greeks, and Romans as a remedy for many ailments, but especially
dropsy (today: congestive heart failure). It was venerated faithfully as general
defense against harm. It was not until our century that the active components of
squill, the glycosides scillaren, and proscillaridin were isolated in their pure form,
and a derivative with improved bioavailability, meproscillarin (Clift®
), was avail-
able for pharmaceutical therapy.
2 I Fundamentals in Drug Research

20. Drug Research: Yesterday, Today, and
Tomorrow 1
The targeted route to medicines is an old dream of humanity. Even the alchemists
sought after the Elixir, the Arcanum that was meant to heal all disease. It still has
not been found today. On the contrary, drug therapy has become even more
complicated as our knowledge of the different disease etiologies has become
more complex.
Nonetheless, the success of drug research is impressive. For hundreds of years,
alcohol, opium, and solanaceae alkaloids (from thorn apples) were the only prepa-
ratory measures for surgery. Today general anesthesia, neuroleptanalgesia, and
local anesthetics allow absolutely pain-free surgical and dental procedures to be
carried out. Until this century, plagues and infectious diseases have killed more
people than all wars. Today, thanks to hygiene, vaccines, chemotherapeutics, and
antibiotics, these diseases have been suppressed, at least in industrialized countries.
The dangerously increasing numbers of therapy-resistant bacterial and viral path-
ogens (e.g., tuberculosis) have presented new problems and make the development
of new medications urgently necessary. The H2-receptor inhibitors and proton-
pump inhibitors have drastically reduced the number of surgical procedures to treat
gastric and duodenal ulcers. Combinations of these inhibitors with antibiotics have
brought even more advances in that it allows a causal therapy (▶ Sect. 3.5).
Cardiovascular diseases, diabetes, and psychiatric diseases (diseases of the central
nervous system, CNS) are treated mostly symptomatically, that is, the cause of the
disease is not addressed, but rather the negative effects of the disease on the
organism. Often the therapy is limited to slowing the progression of these diseases
or increasing the quality of life. Synthetic corticosteroids have lead to significant
pain reduction and retardation of the pathological bone degeneration associated
with chronic inflammatory diseases (e.g., rheumatoid and chronic polyarthritis).
The spectrum of cancer therapy ranges from healing, particularly in combination
with surgical and radiation therapy, all the way to complete failure of all therapeutic
measures.
The history of drug research can be divided into several sequential phases:
• the beginning, when empirical methods were the only source of new medicines,
• targeted isolation of active compounds from plants,
G. Klebe, Drug Design, DOI 10.1007/978-3-642-17907-5_1,
# Springer-Verlag Berlin Heidelberg 2013
3

21. • the beginning of a systematic search for new synthetic materials with biological
effects and the introduction of animal models as surrogates for patients,
• the use of molecular and other in vitro test systems as precise models and as
a replacement for animal experiments,
• the introduction of experimental and theoretical methods such as protein
crystallography, molecular modeling, and quantitative structure–activity rela-
tionships for the targeted structure-based and computer-supported design of
drugs, and
• the discoveries of new targets and the validation of their therapeutic value
through genomic, transcriptomic, and proteomic analysis, knock-in and knock-
out animal models, and gene silencing with siRNA.
Each preceding phase loses its importance with the arrival of the next phase.
Interestingly, in modern drug research individual phases run in the opposite direc-
tion. That is, first a target structure is discovered in the sequenced genome of an
organism and its function is modulated to validate it as a candidate for drug therapy.
Then the structure-based and computer-aided design of an active substance is
undertaken in close cooperation with multiple in vitro tests to clarify the activity
and the activity spectrum. Next, the animal experiments substantiate the clinical
relevance, and in the final step clinical trials confirm a test substance’s suitability as
a medicine for patients.
1.1 It All Began with Traditional Medicines
The beginnings of drug therapy can be found in traditional medicines. The narcotic
effect of the milk of the poppy, the use of autumn crocus (Colchicum autumnale)
for gout, and the diuretic effect of squill (Urginia maritime) for dropsy (today:
congestive heart failure) have been known since antiquity. The dried herbs and
extracts from these and other plants have served as the most important source of
medicines for more than 5,000 years. The oldest written records of these uses are
from 3000 BC.
Around 1550 BC the ancient Egyptian Papyrus Ebers listed approximately 800
prescriptions, of which many contained additional rituals to invoke the help of the
gods. The five-volume book De Materia Medica of Dioskurides (Greek physician,
first century AD) is the most scientifically rigorous work of antiquity. It contains
descriptions of 800 medicinal plants, 100 animal products, and 90 minerals. Its
influence reached into the late Arabic medicine and the early modern age.
The most famous medicine of antiquity was undoubtedly Theriac. Its precursor,
Mithridatum, served the King of Pontus, Mithridates VI (120–63 BC) as an antidote
for poisonings of all kinds. Theriac can be traced to Andromachus, the private
physician of the emperor Nero, and originally contained 64 ingredients. This
preparation remained very widespread even into the eighteenth century. It was
prepared in many variations with up to 100 ingredients. In some cities it was even
prepared under state control to ensure that none of the ingredients were left out! Its
use evolved into a panacea for all diseases. In addition, every imaginable wonder
4 1 Drug Research: Yesterday, Today, and Tomorrow

22. drug was in use, some examples include rain worm oil, unicorn powder, gastric
calculus stones, human cranium powder (Lat. Cranium, skull), mummy dust, and
many more.
Traditional Chinese medicine was very advanced even in ancient times.
A special feature of their formulation was, and is, the circumstances responsible
for the effect of four different qualities. The chief (jun) is the carrier of the effect,
the adjutant (chen) supports the effect or induces a different effect. The assistant
(zuo) can also support the main effect or can serve to ameliorate side effects, and
one or more messengers (shi) moderate the desired effect. The Chinese Pen-Ts’ao
school (first and second century AD), whose goal it was to live for as long as
possible without aging (!), recommended the following dosing regime:
When treating a disease with a medicine, if a strong effect is desired, one should begin with
a dose that is not larger than a grain of millet. If the disease is healed, no more medicine
should be given. If the disease is not healed, the dose should be doubled. If that does not
heal the disease, the dose should be increased tenfold. When the disease is healed, the
therapy should always be discontinued.
The Chinese Materia Medica published by Li Shizhen in 1590 is made up of
52 volumes. It contains almost 1,900 medical principles, plants, insects, animals,
and minerals incorporated into 10,000 detailed recipes for their preparation. The
Chinese Pharmacopeia from 1990 contains only two volumes. One of those
volumes contains 784 traditional medicines; the other contains 967 medications
from “Western” medicine.
Paracelsus (born Theophrastus Bombastus von Hohenheim; 1493/1494–1541)
made a great breakthrough for scientific medical research. He understood the
human to be a “chemical laboratory” and held the ingredients of drugs themselves,
the Quinta essentia, responsible for their healing effects. Despite this, up until
the beginning of the nineteenth century all therapeutic principles were based on
either extracts from plant, animal ingredients, or minerals; only in the most seldom
cases were pure organic compounds used. That changed fundamentally with the
advent of organic chemistry. The great age of natural products from plants (for
examples see 1.1–1.9, Fig. 1.1), and the active substances that were derived from
them had begun. Premature hopes that were invested in some of these substances
around the turn of the previous century, for example in heroin (▶ Sect. 3.3), or
cocaine (▶ Sect. 3.4), were very quickly squelched, but natural products from
plants established the fundamentals for, and form an exceedingly large part of our
modern pharmacy. Natural products and their analogues and derivatives are also
well represented among the best-selling drugs today.
1.2 Animal Experiments as a Starting Point for Drug Research
The wealth of experience gained by traditional medicine is based on many thou-
sands of years of sometimes accidental, sometimes intentional observations of their
therapeutic effects on humans. Planned investigations on animals were relatively
seldom. The biophysical experiment of Luigi Galvani, an anatomy professor in
1.2 Animal Experiments as a Starting Point for Drug Research 5

23. O
HO
H
H
N
N N
N
H3C
CH3
O
O
Morphine
1.1
HO
N
H
N N
CH3
O
Caffeine
1.2
MeO
N
HO
H
N
NHCOMe
O
OMe
MeO
MeO
MeO
N
N COOCH3
O O
H3C
H3C
OH
N
CH3
Quinine
1.3 1.4 Colchicine
H
H
N
H
CH3
Ephedrine
Cocaine
1.6
1.5
H
O
O
OH
Coniine
1.7
N
N
O
H
H
H
MeO Atropine (racemate)
1.8
H
O
OMe
OMe
OMe
OMe
O
MeO
1.9 Reserpine
N CH3
H
Fig. 1.1 Many important natural products were isolated in the nineteenth century, and a few were
synthesized. Morphine 1.1 was isolated from opium by Friedrich Wilhelm Adam Sert€
urner in
1806, caffeine 1.2 was isolated from coffee, and quinine 1.3 was isolated from cinchona bark by
Friedlieb Runge in 1819. Quinine was discovered independently by Pierre Joseph Pelletier and
Joseph Bienaimé Caventou, who one year later isolated colchicine 1.4 from autumn crocus.
Cocaine 1.5 was extracted from coca leaves by Albert Niemann in 1860, and ephedrine 1.6 was
extracted from the Chinese plant Ma Huang (Ephedra vulgaris) by Nagayoshi Nagai. In 1886 the
first alkaloid, coniine 1.7, which is found in hemlock, was synthesized by Albert Ladenburg; in
1901 atropine 1.8 from Deadly Nightshade was synthesized by Richard Willst€
atter. Reserpine 1.9,
from Rauwolfia serpentina was first prepared in the middle of the twentieth century, and its
structure was elucidated.
6 1 Drug Research: Yesterday, Today, and Tomorrow

24. Bologna, which was first described in his book De viribus electricitatis in motu
musculari in 1791, has become famous. In 1780 his students had already observed
how frog thighs would twitch when the nerve was dissected and if a static electricity
generator was simultaneously in use, such devices were standard laboratory equip-
ment in many laboratories at the time. He wanted to demonstrate in standardized
experiments whether the twitching was also caused by thunderstorms. He hung the
legs on an iron window grill with a copper hook — they twitched simply upon
contact with the grill. The voltage difference between the two metals was enough to
stimulate the nerve, even without an electrical discharge.
The systematic investigation of the biological effects in animals of plant
extracts, animal venoms, and synthetic substances began in the next-to-last century.
In 1847 the first pharmacology department was founded at the Imperial University
in Dorpat (today: Tartu, Estonia). The famous pharmacologist, Sir James W. Black,
who developed the first b-blocker (an antihypertensive, ▶ Sect. 29.3) at ICI, and
later took part in the development of the first H2 antagonists (see gastrointestinal
ulcer medications, ▶ Sect. 3.5) at Smith, Kline & French, compared pharmacolog-
ical testing to a prism: what pharmacologists see in their substances’ properties
directly depends on the model that was used to test the substances.
Just as a prism would, the models distort our vision in different ways. There is no
such thing as a depressed rabbit or a schizophrenic rat. Even if there were such
animals, they would not be able to share their subjective perceptions and emotions
with us. Gene-modified animals (▶ Sect. 12.5), such as the Alzheimer mouse, are also
approximations of reality that have been distorted through a different prism, to use
Black’s analogy. This actuality is often underestimated in industrial practices. Sci-
entists tend to optimize their experiments on a particular, isolated model. In doing so,
many factors and characteristics that are essential for a medicine, for instance the
selectivity or bioavailability, are inadequately considered.
There is no way out of this dilemma. We need simple in vitro models (Sect. 1.5)
to be able to test large series of potentially active compounds, and we need the
animal models to correlate the data and to make predictions about the therapeutic
effects on humans. In the past, therapeutic progress was preferentially achieved
when a new in vivo or in vitro pharmacological model was available for a new effect
(see the H2 receptor antagonists, ▶ Sect. 3.5).
Typical mistakes in the selection of models and interpretation and comparison of
experimental results arise from different modes of application and the correlation of
results obtained in different species of animals. It does not make sense to optimize
the therapeutic range of a substance in one species, and the toxicology in another.
Further, comparing effects after a fixed dose, without determining an effective dose
also distorts the results because very strong and weak substances fall outside the
measurement range. Measuring the effect strictly according to a schedule is also
questionable because neither the latency period, that is the time before an effect is
seen, nor the time of maximum biological effect are recorded. In whole-animal
models, auxiliary medications are usually applied, which can also influence the
experimental results. Anesthetized animals often give entirely different results than
conscious animals.
1.2 Animal Experiments as a Starting Point for Drug Research 7

25. 1.3 The Battle Against Infectious Disease
Plagues and infectious diseases, and at the top of this list are malaria and tubercu-
losis, have killed more people over the ages than all of the wars in the history of
humanity. Twenty-two million people died during the first wave of the 1918
influenza (“Spanish flu”). Up until the middle of the twentieth century, millions
of people died every year of malaria, and unfortunately, today these numbers are
shooting up again (▶ Sect. 3.2). Until the turn of the twentieth century, ipecac
(Psychotria ipecacuanha) and cinchona (Cinchona officinalis L.) were the only
therapeutic approaches to this disease. The impressive successes in the fight against
plagues came in large part from the last 80 years of drug research. We have the
sulfonamides (▶ Sect. 2.3) and their combinations with dihydrofolatereductase
inhibitors (▶ Sect. 27.2), the antibiotics (▶ Sects. 2.4, ▶ 6.4, and ▶ 32.6), and
the synthetic tuberculostatic medicines (▶ Sect. 6.5) to thank for this. When
Selman A. Waksman (1888–1973) received the Nobel Prize for the discovery of
streptomycin (▶ Sect. 6.4), a little girl congratulated him with a bouquet of
flowers. She was the first patient with meningeal tuberculosis to be healed with
streptomycin. Today we cannot appreciate the atmosphere in a tuberculosis hos-
pital from our own experience, rather solely from Thomas Mann’s The Magic
Mountain (German: Zauberberg).
However, the infectious diseases, including tuberculosis, are on the advance
again. In the past many antibiotics were too broadly used. This and the spread of
resistant pathogens in hospitals have led to the situation that many cases are only
treatable with very specific antibiotics. If resistance develops to these antibiotics, all
of our weapons are dull. New viral infections are looming. Before the advent of the
immune disease AIDS (acquired immune deficiency syndrome) there were very
few cases of pneumonia from the fungus Pneumocystis jirovecii (formerly
Pneumocystis carinii), nowadays the numbers have increased tremendously. This
type of pneumonia is the primary cause of death of AIDS patients and
immunosupressed patients after organ transplantation. A great effort has been
made to find drugs for AIDS and its complications. On the other hand, many
widespread tropical diseases, for instance malaria and Chagas disease, have been
inadequately researched, and expanding resistance to the currently available med-
ications represents an increasing worldwide problem. Because these diseases are
rampant in parts of the world where people lack the economic resources to finance
chemotherapy, more and more pharmaceutical companies have withdrawn from
these research areas for financial reasons. The chances of recovering the develop-
ment costs from this social stratum are poor. Here the global politics must establish
some structure so that these people are able to benefit from the technological
progress made by modern drug research. An example of this is the Bill and Melinda
Gates Foundation, which is dedicated to the treatment and eradication of diseases
around the entire world, but with particular emphasis on developing countries.
Improved hygiene has also helped to reduce the risk of infection, for
instance traumatic fever or Shigella dysentery (discussed in ▶ Chap. 21, “A Case
8 1 Drug Research: Yesterday, Today, and Tomorrow

26. Study: Structure-Based Inhibitor Design for tRNA-Guanine Transglycosylase”).
Above all else, it was the vaccines that contributed to the eradication of many
infectious diseases. Now as before, hopes rest on new and combined vaccines for
the prevention of AIDS, malaria, and gastrointestinal ulcers, the latter of which we
now know to be caused by the bacteria Helicobacter pylori (▶ Sect. 3.5).
1.4 Biological Concepts in Drug Research
Acetylcholine 1.10 (Fig. 1.2), which was synthesized in 1869 by Adolf v. Bayer, is
a neurotransmitter, that is, a transfer agent for nerve impulses. In 1921 Otto
Loewi, a pharmacologist, proved its biological effect in an elegant experiment.
Two isolated frog hearts were perfused with the same solution. The vagal nerve of
one of the hearts was stimulated, leading to a slowing of the heart rate, a so-called
bradycardia. Shortly afterward, the second heart also began to beat more slowly,
which was a clear indication of a humoral (Lat. humor, umor, fluid) signal transfer.
Soon after that acetylcholine was recognized as the responsible “Vagus Stoff”.
Acetylcholine is itself not usable as a therapeutic because it is metabolized too
quickly by acetylcholine esterases (▶ Sect. 23.7).
In 1901 Thomas Bell Aldrich (1861–1938) and Jokichi Takamine isolated the
first human hormone, adrenaline 1.11 (Fig. 1.2). This hormone and its N-desmethyl
derivative, noradrenaline 1.12 (Fig. 1.2), are produced in a central location, the
adrenal glands, and are released under stress conditions into the entire system with
the exceptions of the CNS and the placenta, which have their own barriers against
most polar compounds. These substances cause different reactions in different parts
of the organism, where they react with the relevant receptors. The specificity is
poor, and a plethora of pharmacodynamic effects result: pulse and blood pressure
rise, and the organism is prepared for “flight” – which has been an exceedingly
important function over the course of evolution.
Noradrenaline and adrenaline (also called norepinephrine and epinephrine,
respectively) are also neurotransmitters (▶ Sect. 29.3), just like acetylcholine, the
biogenic amines 1.13–1.15, the amino acids 1.16–1.19, and peptides, such as 1.20
and 1.21 (Fig. 1.2). Neurotransmitters are produced locally in the nerve cells,
stored, and upon stimulation of the nerve, released. After interaction with receptors
on the neighboring nerve cell, they are quickly metabolized or taken up again by the
same neuron that released them. Depending on the name of the neurotransmitter,
one speaks of the adrenergic, cholinergic, and dopaminergic (etc.) systems. The
effect that adrenaline invokes is referred to as adrenergic, and an antagonist to this
system is called antiadrenergic. However, this nomenclature is not always strictly
adhered to. It is common to see combinations of the name of the neurotransmitter
with the term agonist or antagonist, or sometimes blocker instead of antagonist, for
instance a dopamine agonist, a histamine antagonist, or a b-blocker for antagonists
of b-adrenergic receptors. A plethora of drugs have arisen from the structural
variations of neurotransmitters.
1.4 Biological Concepts in Drug Research 9

27. At the end of the 1920s the steroid hormones were isolated, and their structures
were determined in short order (▶ Sect. 28.5). Altogether the discoveries of the
mid-twentieth century heralded the “golden age” of drug research. The systematic
variation of the principles responsible for biological activity and our increasing
knowledge of the mode of action has led to the synthesis of enzyme inhibitors,
receptor agonists and antagonists, which together with natural product derivatives
from plants makes up the largest part of our modern pharmacy.
+
H3C O
N
CH3
CH3
CH3
O OH
N
R
HO
H
1.10 Acetylcholine
1.11 Adrenaline, R = CH3
HO
NH2
HO
HO
1.12 Noradrenaline, R = H
1.13 Dopamine
HO
NH2
H
1.15
1.14 Histamine
N
N
N
NH2
H
Serotonin
HOOC
HOOC
NH2
COOH
NH2
COOH
1.17 Glutamic acid
1.16 Aspartic acid
1.18 Glycine 1.19 γ-Aminobutyric acid
H2N COOH H2N COOH
Tyr-Gly-Gly-Phe-Met
Tyr-Gly-Gly-Phe-Leu
1.20 Met-Enkephalin
1.21 Leu-Enkephalin
Fig. 1.2 The natural hormones und neurotransmitters acetylcholine 1.10, adrenaline 1.11, nor-
adrenaline 1.12, dopamine 1.13, histamine 1.14, and serotonin 1.15, the excitatory amino acids
glutamic acid 1.16 and aspartic acid 1.17, the inhibitory amino acid glycine 1.18 and
g-aminobutyric acid (GABA) 1.19, and several peptides, such as the enkephalins 1.20 and 1.21,
substance P and others serve as lead structures for drugs for a variety of cardiovascular and CNS
diseases (see ▶ Chaps. 3, “Classical Drug Research”; ▶ 29, “Agonists and Antagonists of Mem-
brane-Bound Receptors”; and ▶ 30, “Ligands for Channels, Pores, and Transporters”).
10 1 Drug Research: Yesterday, Today, and Tomorrow

28. 1.5 In Vitro Models and Molecular Test Systems
Around 40 years ago, we began to think about testing substances in simple in vitro
models. With these models biological testing takes place in test tubes rather than
animals. There are many compelling reasons to avoid animal experiments. They
increasingly provoke public criticism and are time and cost intensive. In the
beginning cell culture models were preferentially employed, for example tumor
cell cultures for testing cytostatic therapies, or embryonic chicken heart cells for
cardio-active compounds. Later these were joined by receptor-binding studies. The
first molecular test models were enzyme-inhibitor assays in which the inhibitory
activity of a molecule could be evaluated on one particular target protein in the
absence of interfering side effects (▶ Chap. 7, “Screening Technologies for
Lead Structure Discovery”). With the progress of gene technology methods
(▶ Chap. 12, “Gene Technology in Drug Research”), not only is the preparation
of the enzyme simplified, but also receptor-binding studies can be carried out on
standardized materials. Today it is possible to achieve an exact evaluation of the
entire activity spectrum of any substance on any enzyme, receptors of all types and
subtypes, ion channels, and transporters. In the meantime, in industrial drug dis-
covery this procedure has become routine. Before biological screening begins, the
following questions have to be answered: what therapeutic goal should be achieved
and is this goal achievable? Therapeutic concepts are established based on the
pathophysiology and the causes of its alteration. Regulatory interventions with
drugs should re-establish the normal physiological conditions as closely as possible.
In doing so, a distinct problem occurs. Nature works on two orthogonal principles: the
specificity of the mode of action and an accentuated spa separation of effects;
the compartmentalization. Adrenaline that is produced in the adrenal glands works
on the entire body except for the brain. If it is released there, it works only in the
synapse between two nerve cells. As far as the specificity goes, the chemists can beat
nature most of the time, but they fail when it comes to spatial separation by a wide
margin.
Through the progress made in gene technology (▶ Chap. 12, “Gene Technology
in Drug Research”) we can investigate active substances much more exactly than
before; but by using isolated enzymes and binding studies we are a long way away
from the reality of animal models, and even further away from humans. In analogy
to the difference between an animal experiment and an isolated-organ experiment,
a well-established correlation between the results obtained in cell culture and an
in vitro test and the desired therapeutic effect is a prerequisite to successfully using
the in vitro model. The quantitative relationship between different biological effects
(▶ Chap. 18, “Quantitative Structure–Activity Relationships”) establishes the con-
nection between animal models and humans.
One modern researcher stands out in the area of CNS-active compounds
especially, but also in areas of cardiovascular-active compounds and antihista-
mines. Paul Janssen (1926–2003) was the director of the company Janssen
Pharmaceuticals in Beerse, Belgium. In the years after World War II, his company
discovered over 70 new active substances, carried out the preclinical and clinical
1.5 In Vitro Models and Molecular Test Systems 11

29. development, and established them as therapies. In doing so, his company
established itself as the most successful in pharmaceutical history. His recipe
for success was not a secret. Paul Janssen was a master of structural variation,
a Beethoven of drug discovery. The systematic combination of pharmacologically
interesting structural fragments, and the elegant evaluation of receptor-binding
studies, in vitro models, and animal experiments were the foundation of
his successes.
1.6 The Successful Therapy of Psychiatric Illness
Up until the middle of the last century psychiatric hospitals were purely custodial care
facilities; they were almost indistinguishable from prisons in terms of the restriction of
personal freedom of the individual. The discovery of neuroleptics, antidepressants,
anticonvulsives, and sedatives revolutionized psychiatry. Typical examples of this
class of drugs are depicted in Fig. 1.3. With the repertoire of drugs that are available
today, schizophrenia, chronic anxiety, and depression preponderate open-ward psychi-
atry. Many patients can be treated in an ambulatory setting. In 1933 Manfred Sakel
(1901–1957), who worked at the psychiatric university hospital in Vienna, noticed that
when schizophrenics were given insulin to stimulate their appetites, they became
calmer. Encouraged by this result, he increased the dose to the point of hypoglycemic
coma, which is a form of deep unconsciousness induced by too little blood sugar. Insulin
shock, pentetrazole, and electroshock became the standard treatment over the next two
decades for psychotic illness, an impressive and frightening proof of the absence of
therapeutic alternatives.
This situation changed in the 1950s with the discovery of reserpine 1.9 (Fig. 1.1,
Sect. 1.1), a herbal natural product. This substance exerts its effect by emptying the
reserves of the neurotransmitters noradrenaline, serotonin, and dopamine in nerve
cells. Reserpine was the first substance to display a prominent neuroleptic effect,
that is, it is sedating and calming, and it was the first compound to be used for
psychotic illness, for which the biological effect could be explained by a mode of
action. In addition, reserpine was used as an antihypertensive medication. Because
of its very broad and unspecific effect it is rarely used today for psychiatric illness
or arterial hypertension.
The role of dopamine 1.13 (Fig. 1.2, Sect. 1.4) in the etiology of schizophrenia
became clear with the discovery of chlorpromazine 1.22 (Fig 1.3, ▶ Sects. 8.5 and
▶ 19.10), a substance that showed a favorable clinical effect. In contrast to the
unspecific reserpine, chlorpromazine is a pure dopamine antagonist. The applica-
tion of chlorpromazine and analogous tricyclic neuroleptics caused symptoms that
occur in Parkinson’s disease. This was the first indication that an endogenous
dopamine deficiency is the cause of that disease.
Chlordiazepoxide (Librium®
, ▶ Sect. 2.7), the first tranquilizer of the group of
benzodiazepines, was found by accident. Only one year after its introduction and
for many years after that, the chemically closely related medication diazepam 1.23
(Valium®
, Fig. 1.3) was the worldwide best-selling drug. The Rolling Stones
12 1 Drug Research: Yesterday, Today, and Tomorrow

30. commemorated it in their multifaceted song “Mother’s Little Helper.” Many com-
panies started grandly endowed synthetic programs, and chemists and pharmacol-
ogists applied their entire arsenal of methods. Their success justified their efforts.
Substances with different modes of action resulted: further tranquilizers, sedatives,
hypnotics, and even antagonists. Even today the benzodiazepines (▶ Sect. 30.5)
belong to the most popular and widespread medications.
The first antidepressant, iproniazid (▶ Sects. 6.7 and ▶ 27.8) was also an acci-
dental discovery. It works by inhibiting the metabolism of the biogenic amines
dopamine, serotonin, noradrenaline, and adrenaline by inhibiting the enzyme
monoamino oxidase (▶ Sect. 27.8). In addition to other severe side effects, the first
unspecific representatives caused hypertensive crises, and when taken with certain
foods a few fatalities occurred. Tyramine, a substance found in cheese, wine, and beer
(therefore the term “cheese effect”) was not duly metabolized. This caused a life-
threatening rise in noradrenaline, a hormone that raises blood pressure.
The antidepressant imipramine 1.24 (Fig. 1.3, ▶ Sect. 8.5) resulted from the
synthesis of analogues of chlorpromazine. Interestingly and despite its close struc-
tural relationship, it is not a neuroleptic but rather it works in the opposite way.
It blocks the transporter for noradrenaline and serotonin, and this prevents the
N
N
CH3
R
O
N
CH3
F3C
N
S
N
CH3
CH3
Cl
N
N
Cl
O
CH3
1.24 Imipramine, R = CH3
1.25 Fluoxetine
Desipramine, R = H 1.26
1.23 Diazepam
Chlorpromazine
1.22
H
Fig. 1.3 A revolution in the therapy of psychiatric illness was brought about by the discovery of
potent neuroleptics such as chlorpromazine 1.22, tranquilizers such as diazepam 1.23, and
antidepressants such as imipramine 1.24. For the first time, these compounds allowed
a purposeful treatment of schizophrenia, chronic anxiety, and depression. Examples of newer
antidepressants with specific modes of action on transport systems (▶ Sect. 4.6) for noradrenaline
and serotonin are desipramine 1.25 and fluoxetine 1.26, respectively.
1.6 The Successful Therapy of Psychiatric Illness 13

31. reuptake of these neurotransmitters from the synaptic gap. Desipramine 1.25 and
fluoxetine 1.26 are even more selective in that they inhibit only the noradrenaline or
the serotonin transporter of nerve cells.
1.7 Modeling and Computer-Aided Design
An extremely capable tool is available for modeling the properties and reactions of
molecules, and particularly their intermolecular interactions: the computer. In
addition to processing complex numerical problems, it is the translation of the
results into color graphics that exceedingly accommodates the human ability to
grasp pictures faster and more easily than text or columns of numbers. That is not
a surprise. Our brains process text sequentially, but pictures are comprehended in
parallel. X-ray crystallography and multidimensional NMR spectroscopic tech-
niques (▶ Chap. 13, “Experimental Methods of Structure Determination”) contrib-
ute to our understanding of molecules as much as quantum mechanical and force
field calculations (▶ Chap. 15, “Molecular Modeling”).
Is molecular modeling an invention of modern times? Yes and No. Friedrich
August Kekulé (1829–1896) supposedly derived his cyclic structure for benzene
from a vision of a snake that circled upon itself and bit its own tail (incidentally, the
snake Uroborus is an age-old alchemist symbol). This now-famous dream may be,
however, traced to a memory of the book Constitutionsformeln der Organischen
Chemie by the Austrian schoolteacher Joseph Loschmidt (1821–1895; Fig. 1.4).
Loschmidt admittedly would take pleasure in contemplating pictures of models that
are quite similar to his own. More and more today we place the three-dimensional
structure, the steric dimensions, and the electronic qualities of molecules in the
foreground. Advances in theoretical organic chemistry and X-ray crystallography
have made this possible. The first structure-based design was carried out on
hemoglobin, the red blood pigment, in the research group of Peter Goodford.
Hemoglobin’s affinity for oxygen is modulated by so-called allosteric effector
molecules that bind in the core of the tetrameric protein. From the three-
dimensional structure he deduced simple dialdehydes and their bisulfite addition
products. These substances bind to hemoglobin in the predicted way and shift the
oxygen-binding curve in the expected direction.
The first drug developed by using a structure-based approach is the antihy-
pertensive agent captopril, an angiotensin-converting enzyme (ACE) inhibitor
(▶ Sect. 25.4). Although the lead structure was a snake venom, the decisive
breakthrough was made after modeling the binding site. For this, the binding site
of carboxypeptidase, another zinc protease, was used because its three-dimensional
structure was known at the time.
The road to a new drug is difficult and tedious. A nested overview of the interplay
between the different methods and disciplines from a modern point of view is
illustrated in the scheme in Fig. 1.5. In the last few years molecular modeling
(▶ Chap. 15, “Molecular Modeling”) and particularly the modeling of ligand–
receptor interactions (▶ Chap. 4, “Protein–Ligand Interactions as the Basis
14 1 Drug Research: Yesterday, Today, and Tomorrow

32. for Drug Action”), have gained importance. Although modeling is employed
predominantly for the targeted structure modification of lead compounds, it is
also suitable for the structure-based and computer-aided design of drugs
(▶ Chap. 20, “Protein Modeling and Structure-Based Drug Design”) and lead
structure discovery (▶ Sect. 7.6). Examples of these approaches are given in
▶ Chaps. 23, “Inhibitors of Hydrolases with an Acyl–Enzyme Intermediate”;
▶ 24, “Aspartic Protease Inhibitors”; ▶ 25, “Inhibitors of Hydrolyzing
Metalloenzymes”; ▶ 26, “Transferase Inhibitors”; ▶ 27, “Oxidoreductase Inhibi-
tors”; ▶ 28, “Agonists and Antagonists of Nuclear Receptors”; ▶ 29, “Agonists and
Antagonists of Membrane-Bound Receptors”; ▶ 30, “Ligands for Channels, Pores,
and Transporters”; ▶ 31, “Ligands for Surface Receptors”; ▶ 32, “Biologicals:
Peptides, Proteins, Nucleotides, and Macrolides as Drugs”.
In addition to modeling and computer-aided design, structure–activity relation-
ship analysis (▶ Chap. 18, “Quantitative Structure–Activity Relationships”) has
contributed to the understanding of the correlation between the chemical structure
of compounds and their biological effects. By using these methods, the influence
of lipophilic, electronic, and steric factors on the variation of the biological
activity, transport, and distribution of drugs in biological systems could be
systematized for the first time on statistically significant foundations.
H
H
OH
O
H2N NH2
Cl
N N
N
N
N
H
H
Fig. 1.4 Loschmidt’s book Constitutionsformeln der Organischen Chemie (1861) contains struc-
tures that anticipate both the formulation of the benzene ring as well as the modern modeling
structure. Kekulé must have known about this book because he disparaged it in a letter to Emil
Erlenmeyer in January 1862 in that he referred to it as “Confusionsformeln.” Loschmidt did not
become famous for his book, but rather because he carried out an experiment in 1865 that
determined the number of molecules in a mole to be 6.021023
, a constant that was later to be
named after him.
1.7 Modeling and Computer-Aided Design 15

33. 1.8 The Results of Drug Research and the Drug Market
The development of different methods in drug research has already been described
in the last section. Table 1.1 gives a short historical overview of the most prominent
results.
Identification of a
biological target, proof
of principle, molecular
test system
Literature, patents,
competitor products
(‘me too’ research)
Biological concept,
clinical side effects
Screening
Natural products,
synthetics, peptides,
combinatorial
chemistry
Lead structures
Experimental design,
synthetic design
Synthesis
Computer-aided
design: protein
crystallography,
NMR, 3D database
searches, de novo
design
DESIGN CYCLE
Biological
testing Structure—activity
relationships, QSAR,
molecular modeling
Candidate for
further
development
Developmental
substance Drug
Formulation
Fig. 1.5 The way to a drug is long. The upper part of the figure shows routes to lead structures.
The middle part describes the design cycle, which in practically all cases must be repeatedly
reiterated. Each of these phases is described in detail in the following chapters. The result of
iterative optimization is candidates for further development such as preclinical and toxicological
studies. It is from these studies that the actual candidates are selected. Formulation, clinical trials,
and registration then lead to a new medicine. The last phases are not presented in this book.
16 1 Drug Research: Yesterday, Today, and Tomorrow

34. Table 1.1 Important milestones in drug research
Year Substance Indication/Mode of action
1806 Morphine Hypnotic
1875 Salicylic acid Anti-inflammatory
1884 Cocaine Stimulant, local anesthetic
1888 Phenacetin Analgetic and antipyretic
1889 Acetylsalicylic acid Analgetic and antipyretic
1903 Barbiturate Sedative
1909 Arsphenamin Anti-syphilitic
1921 Procaine Local anesthetic
1922 Insulin Antidiabetic
1928 Estrone Female sex hormone
1928 Penicillin Antibiotic
1935 Sulfamidochrysoidine Bacteriostatic
1944 Streptomycin Antibiotic
1945 Chloroquine Antimalarial
1952 Chlorpromazine Neuroleptic
1956 Tolbutamide Oral antidiabetic
1960 Chlordiazepoxide Tranquilizer
1962 Verapamil Calcium channel blocker
1963 Propranolol Antihypertensive (b-blocker)
1964 Furosemide Diuretic
1971 L-DOPA Parkinson’s disease
1973 Tamoxifen Breast cancer (estrogen receptor antagonist)
1975 Nifedipine Calcium channel blocker
1976 Cimetidine Gastrointestinal ulcer (H2 blocker)
1981 Captopril Antihypertensive (ACE inhibitor)
1981 Ranitidine Gastrointestinal ulcer (H2 blocker)
1983 Ciclosporin A Immunosuppressant
1984 Enalapril Antihypertensive (ACE inhibitor)
1985 Mefloquine Antimalarial
1986 Fluoxetine Antidepressant (5-HT-transport inhibitor)
1987 Artemisinin Antimalarial
1987 Lovastatin Cholesterol biosynthesis inhibitor
1988 Omeprazole Gastrointestinal ulcer (H+
/K+
-ATPase inhibitor)
1990 Ondansetron Antiemetic (5-HT3 blocker)
1991 Sumatriptan Migraine (5-HT1B,D agonist)
1993 Risperidone Antipsychotic (D2/5-HT2-blocker)
1994 Famciclovir Antiviral/herpes (DNA polymerase inhibitor)
1995 Losartan Arterial hypertension (ATII antagonist)
1995 Dorzolamide Glaucoma (carboanhydrase inhibitor)
1996 Saquinavir HIV protease inhibitor
1996 Ritonavir HIV protease inhibitor
1996 Indinavir HIV Protease inhibitor
1996 Nevirapine HIV reverse transcriptase inhibitor
(continued)
1.8 The Results of Drug Research and the Drug Market 17

35. The assessment of the efficacy and safety of a drug has reached an extraordi-
narily high standard today. To some extent this development is a bystander in our
goal of finding new medicines, but it is also a hindrance. Acetylsalicylic acid
(Aspirin®
) is without any doubt a valuable drug. Today this compound would
have great difficulty to pass clinical trials. Acetylsalicylic acid is an irreversible
enzyme inhibitor, it has relatively weak efficacy, it causes gastric bleeding in high
doses, and it has a very short biological half-life. Each of these problems would be
a profound argument against its continued development today. It probably would
have already failed in screening. In a risk–benefit analysis however, it is better than
most of the alternatives. Where is the problem? It probably lies in the analytical–
deterministic mindset that dominates science, and therefore also drug research. It is
often overlooked that such an approach deals with a system as complicated and
complex as a human, to whom we apply a drug therapy, cannot always be ade-
quately addressed by all means.
Despite public healthcare systems that constitute a barrier between the supplier
and the consumer, the drug market, with worldwide sales of more than US$880
billion, has strong competition. Two forces affect this market: the state of science
Table 1.1 (continued)
Year Substance Indication/Mode of action
1997 Sibutramine Obesity (uptake inhibitor)
1997 Orlistat Obesity (lipase inhibitor)
1997 Tolcapon Parkinson’s disease (COMT inhibitor)
1998 Sildenafil Erectile dysfunction (PDE5 inhibitor)
1998 Montelukast Broncholytic (leukotriene receptor antagonist)
1999 Infliximab Antirheumatic (TNFa antagonist)
2000 Celecoxib Analgesic (COX-2 inhibitor)
2000 Verteporfin Macular degeneration (photodynamic therapy)
2001 Imatinib Acute myeloid leukemia (kinase inhibitor)
2002 Boscutan Arterial hypertension (endothelin-1 receptor antagonist)
2002 Aprepitant Antiemetic (neurokinin receptor antagonist)
2003 Enfuvirtid HIV fusion inhibitor (oligopeptide)
2004 Ximelagatran Coagulation inhibitor (thrombin inhibitor)
2004 Bortezomib Multiple myeloma (proteasome inhibitor)
2005 Bevacizumab Cytostatic (angiogenese inhibitor)
2006 Natalizumab Multiple sclerosis (monoclonal antibody; integrin inhibitor)
2006 Aliskiren Antihypertensive (renin inhibitor)
2007 Maraviroc HIV fusion inhibitor (CCR5 antagonist)
2007 Sitagliptin Type-II diabetes (DPPVI inhibitor)
2008 Raltegravir HIV integrase inhibitor
2009 Rivaroxaban Oral Anticoagulant (FXa inhibitor)
2010 Mifamurtide Drug against Osteosarcoma (bone cancer)
2011 Fingolimod Immunomodulating drug (multiple sclerosis treatment)
18 1 Drug Research: Yesterday, Today, and Tomorrow

36. and technology and the needs of patients. A few drugs command a large portion of
sales. Constantly changing “hit lists” of the best-selling drugs can be found on the
internet. Because of the merging of established pharmaceutical companies in the
last years, the market has contracted to fewer, bigger companies. It is frequently
the case that a single drug can make or break a company. Often only two to three
drugs make up more than 50% of a large company’s sales. A historical example is
Glaxo. This company made its way out of the midfield to the top with ranitidine.
Astra experienced a similar boom with omeprazole. Today after the merger with
Zeneca, it belongs to the biggest representatives of this field. Sankyo also had
a single drug, lovastatin, that exceedingly boosted sales. With its drugs sildenafil
(Viagra®
) and atorvastatin (Sortis®
/Lipitor®
) Pfizer’s profits shot to unimaginable
highs. Just in the last years we have been able to see an increasing concentration of
pharmaceutical companies, so that the market is making a transition to an oligo-
poly, dominated by multinational corporations. Keep in mind that sales giants such
as GlaxoSmithKline (GSK), Novartis, Sanofi-Aventis, Bayer HealthCare, Bristol-
Myers Squibb or AstraZeneca have only originated in the last 10 years through
mergers. Companies such as Pfizer and Roche have significantly grown from acqui-
sitions. The role research plays for pharmaceutical companies is apparent when one
considers that typically 15–20% of turnover is invested in this area. It is certain that
the concentration of the pharmaceutical market is not complete. We can only wait and
see how the landscape continues to shift and adapt at an almost annual pace.
1.9 Controversial Drugs
Drugs remain in the focal point of public interest. Whereas for decades it was the
physician alone who prescribed medication, today it is the patient, frightened by the
lay press or better informed through labeling or reputable literature, who wants to
take control of, or at least share in the decision making.
The issues can be illustrated by one example. Psychotropic pharmaceuticals
exert an impressive effect on personality and behavior. At least since the intro-
duction of Valium®
(diazepam) these drugs have been in the media spotlight.
They are invaluable for the treatment of psychiatric illness. On the other hand, the
danger of misuse and addiction is particularly high. Some of these drugs are even
used as self-medication, without strict adherence to the indication guidelines.
Fluoxetine 1.26 (Prozac®
, Fig. 1.3, Sect. 1.6) was introduced in 1988 by Eli Lilly,
and brought unequivocal progress in the treatment of depression. On this one
medication alone there are now over ten popular science books with controversial
content. Peter Kramer’s book Listening to Prozac takes an overall sympathetic
tone with the assertion that depressed patients feel better and more “in harmony”
with their personality after treatment with fluoxetine. This book was on the New
York Times bestsellers’ list for over 21 weeks. Peter Breggin’s book Talking Back
to Prozac criticized fluoxetine, the company Eli Lilly, and the U.S. Food and Drug
Administration (FDA) polemically. The side effects, risks, and particularly the
addictive potential were placed in the foreground. Both books contain correct
1.9 Controversial Drugs 19

37. assertions, and both books lead to the wrong conclusions. Prozac®
is a valuable
medicine for the treatment of clinically manifest depression; for the treatment
of mundane unhappiness or as a general stimulant, however, it is a drug with
many risks.
To make a risk–benefit analysis of a medication, it is important to consider not
only the desired effect but also the severity of the illness and the objective and
subjective side effects. In oncology one accepts even severe side effects for the
possibility of improving the patient’s condition. If an end-stage cancer patient is
refused an effective pain therapy because of the risk of addiction, then that must be
seen as malpractice. On the other hand many people handle highly potent medica-
tions recklessly. The misuse of antibiotics, the faith in the almighty power of
tranquilizers and antidepressants, or the chronic use of analgesics and laxatives
do more damage than good.
1.10 Synopsis
• Drug research can be divided into several sequential phases starting with empirical
observations of the uptake of natural products from food, the development of
in vitro test systems, increasing understanding of structures and modes of action,
to in vivo models and gene technology.
• It all started with traditional medicines. The first prescriptions date back to the
ancient Egyptians and to traditional Chinese medicine.
• Paracelsus founded scientific medical research and understood humans to be
a “chemical laboratory.” The ingredients of drugs were first held responsible for
healing effects.
• With the advent of organic chemistry, the first therapeutic principles based on
pure organic compounds became available. The great age of natural products
from plants and their active ingredients began.
• Systematic studies on animals began in the next-to-last century and can be
seen as a starting point for drug research. In vitro models are needed to
test large series of potentially active compounds, but animal models are required
to correlate the data and make predictions about the therapeutic effects
in humans.
• Our present life expectancy would not be possible without the successful
fight against infectious diseases. The broad application of antibiotics and
the spread of resistant pathogens, however, have led to situations in which
the best weapons against infectious diseases are becoming increasingly dull.
Research against widespread tropical diseases has been neglected, and
the currently increasing resistance to available medications represents a
worldwide problem.
• The elucidation of biological concepts, pathways, and regulatory cycles by
endogenous compounds has strongly stimulated drug research. Many developed
drugs have arisen from structural variations of neurotransmitters, hormones,
steroids, or natural substrates.
20 1 Drug Research: Yesterday, Today, and Tomorrow

38. • Systematic substance testing began with the establishment of in vitro models
that replaced biological testing on animals by assays in test tubes. Gene
technology has made it possible to prepare sufficient amounts of pure proteins
for testing.
• The discovery of neuroleptics, antidepressants, anticonvulsives, and sedatives
has revolutionized the treatment of psychiatric diseases.
• Molecular modeling and computer-aided design along with structural
biology give access to rational considerations on drug action. The first
structure-based design project was carried out on hemoglobin, and the first
drug developed by using a structure-based approach was the antihyperten-
sive captopril.
• The assessment of drug efficacy and safety has reached an extraordinary high
standard today. The worldwide drug market, with nearly a thousand billion
US dollars in sales per year, is large and highly competitive. Only a few
drugs command a large portion of the sales and determine the particular
dynamics in the market; the current tendency is corporate contraction to
fewer and bigger companies. Often a single drug can make or break
a company.
• Drugs remain in the focal point of public interest. It is no longer the physician
alone who influences the prescription of medication; multiple sources of infor-
mation have an impact and inform the patient. A proper risk–benefit analysis of
a medication, taking into consideration not only the desired therapeutic effect
but also the severity of an illness, is needed.
Bibliography
General Literature
Barondes SH (1993) Molecules and mental illness, Scientific American Library. W. H. Freeman
and Company, New York
Beddell CR (ed) (1992) The design of drugs to macromolecular targets. Wiley, Chichester
Fischer D, Breitenbach J (eds) (2003) Die Pharmaindustrie. Spektrum Akademischer Verlag,
Heidelberg/Berlin
Friedrich C, Müller-Jahncke W-D (2005) Von der Frühen Neuzeit bis zur Gegenwart, vol 2.
GOVI-Verlag, Eschborn
Higby G (ed) (1997) The inside story of medicine. A Symposium. Madison, Wi
Herrmann EC, Franke R (eds) (1995) Computer-aided drug design in industrial research, Ernst
Schering research foundation workshop 15. Springer, Berlin
Müller K (ed) (1995) De Novo Design, Persp. Drug Discov. Design, vol 3, Escom, Leiden, 1995
MüllerJahnke WD, Friedrich C (2005) Arzneimittelgeschichte. Wissenschaftliche Verlagsge-
sellschaft, Stuttgart
Perun TJ, Propst CL (eds) (1989) Computer-aided drug design. Methods and applications. Marcel
Dekker, New York
Porter R, Teich M (eds) (1995) Drugs and narcotics in history. Cambridge
Restak RM (1994) Receptors. Bantam Books, New York
Schmitz R (1998) Geschichte der Pharmazie, vol 1. GOVI-Verlag, Eschborn
Bibliography 21

39. Verband Forschender Arzneimittelhersteller (2009) e.V.: http://www.vfa.de/de/presse/statcharts/
arzneimittelmarkt/. Accessed 22 Nov 2011
Werth B (1994) The Billion-Dollar Molecule. One Company’s Quest for the Perfect Drug.
Touchstone, New York
Special Literature
Beddell CR, Goodford PJ, Norrington FE et al (1976) Compounds designed to fit a site of known
structure in human hemoglobin. Br J Pharmac 57:201–209
Breggin PR, Breggin GR (1994) Talking back to prozac. St. Martin’s Press, New York
Kramer P (1993) Listening to prozac. Viking, New York
Mutschler E (1987) Arzneimittel – Erfolge, Misserfolge, Hoffnungen. Deutsche Apoth-Ztg
127:2025–2033
Newman DJ, Cragg GM (2007) Natural products as sources of new drugs over the last 25 years.
J Nat Prod 70:461–477
Noe CR, Bader A (1993) Facts are better than dreams. Chem Brit 29:126–128, Kekulés and
Loschmidts Formeln
22 1 Drug Research: Yesterday, Today, and Tomorrow

40. In the Beginning, There Was Serendipity
2
“A lucky accident dropped the medicine into our hands”; this is how a publication on
August 14, 1886, from Arnold Cahn and Paul Hepp in the Centralblatt f€
ur Klinische
Medizin began. The history of drug research is punctuated by lucky accidents.
As a general rule, detailed knowledge of biological systems was absent. So it is not
surprising that the working hypotheses were often wrong, and the obtained results
differed from the expectations. The case of accidental success fell into the back-
ground over time. Today happenstance as a strategy has been replaced by the arduous
and ambitious goal of preparing drugs by using a straightforward approach. The only
exception to this is the kind of shotgun-style testing of large and diverse chemical
compound libraries, including microbial and plant extracts that is done with the goal
of finding new lead structures. In this case, serendipity is desired to find as large and
diverse a palette of lead structures (▶ Chaps. 6, “The Classical Search for Lead
Structures” and ▶ 7, “Screening Technologies for Lead Structure Discovery”) with
potential for further optimization (▶ Chaps. 8, “Optimization of Lead Structures” and
▶ 9, “Designing Prodrugs”).
2.1 Acetanilide Instead of Naphthalene: A New, Valuable
Antipyretic
Back to Cahn and Hepp. What happened? There are several legends about this
lucky accident. The most plausible version is that the antipyretic effect of naph-
thalene, which was widely available from coal tar, was tested. The substance indeed
showed fever-lowering qualities. The responsible substance however, was not naph-
thalene but rather something entirely different: acetanilide 2.1 (Fig. 2.1). Further
experiments confirmed the efficacy. Shortly thereafter, the company Kalle Co.
introduced it to the market with the name “Antifebrin.”
Phenacetin 2.2 (Fig. 2.1) was subsequently developed based upon a targeted
approach. At the time, Bayer in Elberfeld had 30 t of p-nitrophenol, a side product
from dye production, on their waste heap. The then 25-year-old Carl Duisberg, who
later became the chairman of Bayer Farbenfabriken AG and who also took a leading
G. Klebe, Drug Design, DOI 10.1007/978-3-642-17907-5_2,
# Springer-Verlag Berlin Heidelberg 2013
23

41. role in the foundation of I.G. Farbenindustrie in 1924, wanted to use it for the
preparation of acetanilide as it could easily be reduced to p-aminophenol. The
known toxicity of phenol groups led to the design of p-ethoxyacetanilide 2.2 (phen-
acetin), which actually did have the desired qualities and served as an analgesic for
headaches and as an antipyretic for a century. Unfortunately its metabolite 2.4, which
still contains the ethoxy group, leads to the production of methemoglobin, an
oxidized form of the red blood pigment that is incapable of carrying oxygen.
Furthermore, chronic misuse by, for instance, taking kilogram quantities of phenac-
etin over a lifetime, leads to kidney damage. Paradoxically, the main metabolite of
phenacetin, p-hydroxyacetanilide 2.5 (Fig. 2.1, acetaminophen in American English,
or paracetamol in UK English) is actually responsible for the effect, and it is less toxic
and better tolerated. In the USA alone, paracetamol achieved over US$1.3 billion in
annual sales. This is even more than for acetylsalicylic acid.
2.2 Anesthetics and Sedatives: Pure Accidental Discovery
In 1799 Humphry Davy (1778–1829) discovered the euphoric effect of nitrous oxide
(N2O), which was appropriately named “laughing gas.” The dentist Horace Wells
(1815–1848) saw a traveling theater production of a “sniffing party” with N2O in
1844 in which a participant suffered from a flesh wound, apparently without pain. To
test this effect, Wells had one of his own teeth extracted, also without pain. He then
repeated the procedure on many people, with success. A public demonstration went
O
N
O-
O
C
O
+
HN CH3
HN CH3
OH
OEt
Phenacetin
O
p-Nitrophenol
Acetanilide
2.1 2.2 2.3
NH2 HN CH3
OEt OH
2.4 2.5 Paracetamol
Toxic metabolite
Fig. 2.1 By starting with the accidently discovered acetanilide 2.1, Carl Duisberg planned
the synthesis of phenacetin 2.2 from nitrophenol 2.3. In contrast to the toxic metabolite 2.4, the
main metabolite, paracetamol (Amer. acetaminophen) 2.5 is well tolerated.
24 2 In the Beginning, There Was Serendipity

42. wrong though, and this drove him to suicide four years later. The same effect was
observed in 1842 by Crawford W. Long (1815–1878) with ether, but he did not report
it immediately. After administering ether, he was able to remove an ulcer from the
neck of a volunteer. William T. Morton (1819–1868) successfully carried out the first
ether anesthesia in the same hospital as Wells. Starting in 1847, chloroform was used
as an anesthetic. A few years later anesthesia became standard for surgical pro-
cedures, a real blessing for the suffering of humanity.
Oskar Liebreich (1839–1908) wanted to develop a depot form of chloroform 2.6
in 1868. Because chloral hydrate can be cleaved with base in an aqueous milieu, he
hoped that this could also happen in the body. Chloral hydrate is in fact a sedative,
but this is because of its active metabolite, trichloroethanol 2.8 (Fig. 2.2), and not
because it releases chloroform.
In 1885 Oswald Schmiedeberg (1838–1921) tested urethane 2.9 (ethylcarbamate,
Fig. 2.3) because he thought that it would release ethanol in the organism. Urethane
itself is the active agent. Its optimization later led to isoamylcarbamate 2.10
(Hedonal®
, 1899). Based on this, open and cyclic carbamates and ureas were
investigated. In 1903 the first barbiturate sedative, barbital (Veronal®
) resulted.
In the decades that followed, a wealth of better-tolerated barbiturates with a broader
pharmacokinetic spectrum was introduced.
2.3 Fruitful Synergies: Dyes and Pharmaceuticals
Dyes and pharmaceuticals have stimulated each other. The first synthetic dye was
the result of a failed drug synthesis. In 1856 August Wilhelm v. Hoffman assigned
the task of synthesizing quinine, an alkaloid used for treating malaria (▶ Sects. 1.1
and ▶ 3.2), to the then 17-year-old William Henry Perkins (1838–1907); by starting
Cl CH
Cl OH
H
Cl
Cl
CH2OH
Cl
Cl
OH−
2.6 Chloroform 2.7 Chloral hydrate 2.8 Trichlorethanol
Metabolism
Cl OH
Cl Cl
Fig. 2.2 The anesthetic chloroform 2.6 is formed upon treatment of chloral hydrate 2.7 with base.
This reaction does not work in vivo, however. The active metabolite of 2.7 is trichloroethanol 2.8.
O
R
2.9 Urethane R = −CH2 CH3
O
H2N
2.10 Isoamylcarbamate
O
H
N
N
O
O
Et
Et
H
2.11 Barbital
R = −CH2CH2CH(CH3)2
Fig. 2.3 The hypothetical
“prodrug” of ethanol,
urethane 2.9, led to the
development of
isoamylcarbamate 2.10,
which in turn led to the first
barbiturate, barbital 2.11.
2.3 Fruitful Synergies: Dyes and Pharmaceuticals 25

43. with only the molecular formula, it was anticipated that the oxidation of an allyl-
substituted toluidine would deliver the desired product. Now that the structural
formula is known, we understand that this could not possibly have worked! Upon
oxidation of aniline that was contaminated with o- and p-toluidine Perkins isolated
a dark precipitate. It contained a dye, mauveine 2.12 (Fig. 2.4) that colored silks
a brilliant mauve. Other dyes were prepared in rapid succession. The development
and later proliferation of the dye industry in England and Germany in the second
half of the nineteenth century can be traced back to this accidental discovery.
Toward the end of the next-to-last century increasing competition and a difficult
economic situation in the dye market inspired the reactionary expansion into
industrial pharmaceutical research. In 1896 a pharmaceutical research laboratory
was founded in the 33-year-old Bayer Farbenfabrik. At that time innumerable
synthetic dyes were known, therefore it is not surprising that these substances
were tested for pharmacological effects.
Of all people, wine adulterators played an important role in the discovery of the
first synthetic laxative. To stop people from selling Trester wine (so-called
Nachwein) as a natural wine (Naturwein), in 1900 the dye phenolphthalein was
added as an easily detectable indicator. The Hungarian pharmacologist Zoltán
von Vámossy (1868–1953) investigated the effects of this compound. Back then,
the conventions of the pharmacologists were still rather primitive. The intravenous
application of 0.01–0.03 g to rabbits caused death “with loud shrieking, convul-
sions, and paralysis”. Vámossy then decided to feed 1–2 g to a rabbit and 5 g to a
4 kg lap dog. Because these oral doses were all well tolerated, Vámossy took 1.5 g
of phenolphthalein himself, and a friend took 1.0 g. The effects were explosive:
rumbling in the bowels, diarrhea, and for two additional days loose stools. It was
later established that 150–200 mg would have been a therapeutic dose.
N
N
H3C
H2N NH
CH3
CH3
NH2
R = H oder o-, p-Methyl
C20H24N2O2 + H2O
3 [O]
[O]
+
2 C10H13N
2.12 Mauveine
Allyl-
toluidin
Quinine
R
Fig. 2.4 An unsuccessful quinine synthesis founded the dye industry. The structures of many
organic compounds were still entirely unknown in the middle of the nineteenth century. The
attempt to prepare quinine via a simple route (upper reaction) could not have worked. The
oxidation of an impure aniline (below) gave mauveine 2.12 in 1856, which was used to dye silk
a brilliant mauve color. It was the first synthetic dye!
26 2 In the Beginning, There Was Serendipity

44. An entire range of antibacterial and antiparasitic dyes are based on the work
of Robert Koch (1843–1910). He showed that bacteria and parasites accumulate
dyes specifically. Based on this, Paul Ehrlich (1854–1915) hoped to kill pathogens
selectively with suitably chosen dyes. In 1891 he cured two mild cases of malaria by
treating the patients with methylene blue. In the following years he tested hundreds of
different pigments, and thousands more analogues were later synthesized in the
laboratories of Bayer and Hoechst. In 1909 Paul Ehrlich pursued a rational design
when he exchanged both of the nitrogen atoms of an —N═N— group of an azodye
for arsenic atoms. Arsphenamine 2.14 (Salvarsan®
, Fig. 2.5) was the first effective
compound to treat syphilis; the first chemotherapeutic. It became an extraordinary
economic success for the company Hoechst.
The breakthrough with chemotherapeutics was made by the physician Gerhard
Domagk (1895–1964). At the age of 31, he took over the newly formed department
of experimental pathology at Bayer in Elberfeld. Azo dyes bearing sulfonamide
groups had already been designed by the chemists Fritz Mietzsch and Josef Klarer,
but they showed no in vitro activity; Domagk tested these substances in strepto-
cocci-infected mice. By using this model, he found the first active substances in
1932. Sulfamidochrysoidine 2.15 (Protonsil®
, Fig. 2.6), a dark-red dye that could
As
HO
H2N
As
NH2
OH
O
O
HO
HO
2.13 Phenolphthalein 2.14 Arsphenamine
x 2 HCl
Fig. 2.5 The laxative effect of phenolphthalein became apparent while testing it as an additive for
cheap wines. The antisyphilis compound arsphenamine 2.14 (Salvarsan®
, here shown as monomer)
is simply an azodye in which the —N═N— group was exchanged for an —As═As— group.
H2N
H2N H2N
N N
NH2
SO2NH2
2.15 Sulfamidochrysoidine
2.16 Sulfanilamide 2.17 p-Aminobenzoic acid
SO2NH2 COOH
Fig. 2.6 The red azodye sulfamidochrysoidine 2.15 is effective only after cleavage to the
colorless sulfanilamide 2.16, which is a bacterial antimetabolite of p-aminobenzoic acid 2.17.
2.3 Fruitful Synergies: Dyes and Pharmaceuticals 27

45. treat even severe streptococci infections, resulted in 1935. The sulfonamides
became world famous a year later when the son of the US president, Theodore
D. Roosevelt, Jr., was treated with one to cure a severe sinus infection. But
even here a false hypothesis led to success. It was not the azodye itself, but rather
its metabolite, sulfanilamide 2.16 that was effective. Sulfanilamide replaces
p-aminobenzoic acid 2.17 (Fig. 2.6), which is needed for the bacterial synthesis
of an enzymatic cofactor, dihydrofolic acid.
2.4 Fungi Kill Bacteria and Help with Syntheses
The discovery of the antibiotic effect of Penicillium notatum by Alexander Fleming
(1881–1955) in 1928 is the most famous example of a serendipitous discovery.
Fleming noticed that a spoiled staphylococcus culture had been contaminated with
a fungal infection. In the area around the fungus, no bacteria could grow. Further
investigations showed that this fungus could also curb other bacteria. Fleming
called the still-unknown agent penicillin. It was not until 1940 that it was isolated
and characterized by Ernst Boris Chain (1906–1979) and Howard Florey (1910–
1985). In 1941 an English policeman was the first patient to be treated with
penicillin. Despite a temporary improvement, and even though penicillin could be
isolated from his urine, he died after a few days as no more penicillin was available
for his continued therapy. The fungus Penicillium chrysogenum, which produces
more penicillin than Penicillium notatum and is easier to cultivate was isolated
from a moldy melon in Illinois. The tedious route to the structural elucidation of
penicillin and the successful work to systematically vary its structure are scientific
masterworks of the first order. There were even more difficult problems to conquer
to optimize its production and its biotechnological mass production. Today the
modified penicillins 2.18 and cephalosporins 2.19 (Fig. 2.7), which make up a broad
range of antibiotics with outstanding bioavailability are available. The newer
analogues have a broader spectrum of activity against many pathogens and are
distinguished by a generally improved stability to the penicillin-degrading enzyme
b-lactamase. Fleming was a researcher to whom Pasteur’s thesis “chance favors the
prepared mind” fully applies. One day in 1921 while working in his laboratory with
a cold, he tried a rather headstrong experiment. He added a drop from his own nasal
mucus to a bacterial culture and found a few days later that the bacteria had been
S
H H CH3
CH3
N
S
H H
RHN
RHN
N
O COOH
O CH2R⬘
COOH
2.18 Penicillins 2.19 Cephalosporins
Fig. 2.7 Fleming’s accidental discovery of the antibiotic effects of a fungus has delivered a wide
palette of penicillins 2.18 and cephalosporins 2.19, each with different R groups.
28 2 In the Beginning, There Was Serendipity

46. killed. This “experiment” led to the discovery of lysozyme, an enzyme that hydro-
lyzes the bacterial wall. As a therapy it is unfortunately unsuitable because it does
not attack most human pathogens.
Chance and a fungus played an important role in the industrial synthesis of
corticosteroids. An important step in the synthesis is the introduction of an oxygen
atom at a particular position in the steroid scaffold, position 11. In 1952 chemists at
the Upjohn company sought after a soil bacteria that could hydroxylate a steroid in
this position. Just when they finally decided to set an agar plate on the window bank
of the laboratory, Rhizopus arrhizus landed exactly there. This fungus transforms
progesterone (▶ Sect. 28.5) to 11a-hydroxyprogesterone. With its help the yield
could be increased to 50%. The closely related fungus Rhizopus nigricans even
afforded 90% of the desired product.
2.5 The Discovery of the Hallucinogenic Effect of LSD
In the 1930s Albert Hoffmann (1906–2008) was working on the partial synthesis of
ergoline alkaloids at Sandoz. In 1938 he wanted to find a way to transfer the
respiratory and cardiovascular stimulatory effect of N,N-diethyl nicotinamide
2.20 onto this class of compounds. In analogy to 2.20, he prepared N,N-diethyl
lysergamide 2.21 (Fig. 2.8) with the hope of maintaining the stimulatory circulatory
and respiratory effects. Except in case the experimental animals were agitated
under anesthesia, the substances showed no particular effect. Therefore they were
not pursued at first. Hoffman prepared the substances for a second time five years
later because he wanted to investigate them more thoroughly. Upon the purification
procedure and recrystallization he reported feeling “a strange agitation combined
with a slight dizziness.” At home he fell into “a not-unpleasant inebriated condition
that was characterized by extremely animated fantasies . . . after about 2 hours, the
condition went away.” Hoffman suspected a connection to the compounds he
prepared and conducted a self-experiment with 0.25 mg a few days later. That
was the smallest dose with which he expected to see an effect. The outcome was
dramatic, the experience was the same as the first time, but much more intense. He
had a technician accompany him home on his bicycle. During the ride, his condition
H
N
CO-N(Et)2
N
CH3
H
H CO-N(Et)2
HN
2.20 N,N-diethyl
nicotinamide
2.21 LSD
Fig. 2.8 N,N-Diethyl nicotinamide 2.20 is a centrally active derivative of nicotinic acid.
Hofmann wanted to synthesize a general stimulant analogously by preparing the N,N-diethyl
amide of lysergic acid. The result was the hallucinogen lysergic acid diethyl amide 2.21 (LSD).
2.5 The Discovery of the Hallucinogenic Effect of LSD 29