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BASIC PRINCIPLES OF DRUG
DISCOVERY AND DEVELOPMENT
BASIC PRINCIPLES OF
DRUG DISCOVERY AND
DEVELOPMENT
SECOND EDITION
BENJAMIN E. BLASS
Temple University School of Pharmacy, Department of Pharmaceutical Sciences,
Moulder Center for Drug Discovery Research, Philadelphia, PA, United States
Academic Press is an imprint of Elsevier
125 London Wall, London EC2Y 5AS, United Kingdom
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The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
Copyright © 2021 Elsevier Inc. All rights reserved.
No part of this publication may be reproduced or transmitted in any form or by any means,
electronic or mechanical, including photocopying, recording, or any information storage and
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with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency,
can be found at our website: www.elsevier.com/permissions.
This book and the individual contributions contained in it are protected under copyright by the
Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and experience
broaden our understanding, changes in research methods, professional practices, or medical
treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in
evaluating and using any information, methods, compounds, or experiments described herein. In
using such information or methods they should be mindful of their own safety and the safety of
others, including parties for whom they have a professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors,
assume any liability for any injury and/or damage to persons or property as a matter of products
liability, negligence or otherwise, or from any use or operation of any methods, products,
instructions, or ideas contained in the material herein.
ISBN: 978-0-12-817214-8
Sir Isaac Newton, one of the greatest scientists of his time, wrote “If I
have seen further it is by standing on the shoulders of Giants.”
Although he was almost certainly referring to his scientific achieve-
ments, the underling concept of learning from our forbearer is true in
any endeavor. Indeed, this concept can be further extended to include
those who are there in the present day, supporting the activities of an
individual as he or she attempts to accomplish that which they view as
important. With this thought in mind, I have dedicated this book to the
scientists who came before me, those who mentored me, and those who
work with me on a daily basis. In addition, and perhaps more impor-
tantly, this text is dedicated to the loving and supportive family that
has helped me become the person that I am today. Special thanks are
offered to my mother, father, sister, brother, my three children, and of
course, my wife Kathleen. These are the giants on whose shoulders I
have stood upon.
Contents
Foreword xv
vii
viii CONTENTS
Distribution 324
Permeability 326
Transporters 328
Plasma protein binding 330
Elimination pathways 332
Metabolism 333
Excretion 345
In vitro ADME model systems 348
In Vivo pharmacokinetics 351
Volume of distribution 353
Clearance 355
Half-life 356
Bioavailability 359
Species selection 362
Questions 362
References 364
The last several decades have witnessed a revolution in the drug dis-
covery and development process. Medicinal chemistry and in vitro
screening that were once major bottlenecks in the process of identifying
novel therapeutics have been dramatically accelerated through the
incorporation of automation and the development of enabling technolo-
gies such as recombinant DNA and transfection technology. High-
throughput screening, parallel synthesis, and combinatorial chemistry
have facilitated the synthesis and biological evaluation of large numbers
of potentially useful compounds. These activities, in turn, have gener-
ated vast amounts of data that can be analyzed to develop structure
activity relationships and structure property relationships useful for the
optimization of lead compounds. At the same time, new techniques,
technological advances, and a greater understanding of the importance
of pharmacokinetics, animal models, and safety studies have dramati-
cally altered how new molecules are selected for clinical study. Clinical
trial design strategies, biomarkers, translational medicine, the regulatory
landscape, intellectual property rights, and the business environment
have also changed dramatically over the course of the last 40 years.
The complexities of the drug discovery and development process
cannot be overstated, nor can the wide range of expertise required for
the successful development of new, marketable therapeutics. In order to
thrive in this very changing landscape, individuals interested in a career
in the pharmaceutical industry or related fields must be more than sim-
ply experts in their chosen field of study. They must also have an
understanding of the numerous, overlapping fields of their colleagues.
Basic Principles in Drug Discovery and Development has captured the criti-
cal information on the disparate processes, technologies, and expertise
required for modern drug discovery and development and presents it
in a logical and concise manner for students, practicing scientists, and
nonscientist with an interest in the pharmaceutical industry. Dr.
Benjamin E. Blass, an experienced educator and scientist with founda-
tional knowledge in medicinal chemistry, drug design, biological tar-
gets, and over 25 years of experience in industrial and academic drug
discovery and development, provides a comprehensive account of the
many functions involved in drug discovery and development, from
xv
xvi Foreword
1
Drug discovery and
development: An overview of
modern methods and principles
Over the course of the last two centuries, modern medicines have
improved the lives of countless patients. Diseases and conditions that
were once deemed incurable or fatal have been conquered with thera-
peutic agent designed to extend and improve quality of life. The most
recent, and perhaps most notable of these accomplishments is the transi-
tion seen in the consequences of infection with human immuno-
deficiency virus (HIV), the virus known to cause acquired
immunodeficiency syndrome (AIDS).1 When the virus was first identi-
fied by two research groups in 1983,2 there were few antiviral agents
available, none provided effective treatment for HIV infection, and
infection progressed rapidly to AIDS and death by opportunistic infec-
tion. By 1987, AZTs (Retrovirs and Azidothymidine; Fig. 1.1), the first
nucleoside reverse transcriptase inhibitor (NRTI), was approved for
clinical application for the treatment of HIV infection,3 and additional
treatment options were developed through the next three decades. New
NRTIs such as Vireads (Tenofovir)4 and Zeffixs (Lamivudine)5
(Fig. 1.1) that shared AZT’s mechanism of action (phosphorylation,
incorporation into a growing DNA chain, and chain termination)
expanded this class of HIV drugs. The development of non-NRTIs such
as Viramunes (Nevirapine)6 and Doravirines (Pifeltro)7 (Fig. 1.1) fur-
ther advanced HIV therapy and demonstrated that reversible, allosteric
inhibition (enzyme inhibition accomplished through drug binding at a
site other than the catalytic site, see Chapter 3) of reverse transcriptase
was a viable approach. HIV protease inhibitors such as Viracepts
(Nelfinavir),8 Norvirs (Ritonavir),9 and Crixivans (Indinavir)10 entered
the market at the beginning in the mid-1990s, adding a new dimension
to HIV therapy. At the same time, multidrug cocktail treatment
NH2 O
OH O
H HN
N N S N O CN
O H N NH2 N
HO OH HN
N O N P O N N
N N
N3 NH O O O N N CF3
O OH O
Cl
® ®
AZT Viread® Zeffix Viramune® Doravirine®
(Retrovir) (Tenofovir) (Lamivudine) (Nevirapine) (Pifeltro)
O
O
N N OH HN O
S HN O H O
O HO NH
O S
N N N
N N O N H
H H N OH N
OH H
S
H
OH
Viracept® Norvir® Crixivan® N
FIGURE 1.1 Reverse transcriptase was the first enzyme successfully targeted in a drug
discovery program that focused on developing treatment options for HIV infection and
AIDS. AZTs (Retrovir), Vireads (Tenofovir), and Zeffixs (Lamivudine) are nucleoside
inhibitors of this important enzyme that terminate DNA chain growth, while Doravirines
(Pifeltro) is a non-nucleoside inhibitor of reverse transcriptase that reversibly binds to an
allosteric site of the target. HIV protease, another enzyme critical to the progression of
HIV and AIDS, has also been the subject of intense study. The antiviral agents Viracepts
(Nelfinavir), Norvirs (Ritonavir), and Crixivans (Indinavir) are HIV protease inhibitors
that were developed for the treatment of HIV infection and AIDS. HIV integrase inhibitors
such as Raltegravirs (Isentress), Dolutegravirs (Tivicay), and Bictegravirs (GS-9883) were
also developed for the treatment of HIV. AIDS, Acquired immunodeficiency syndrome;
HIV, human immunodeficiency virus.
O H2N O
P
H H
N N N N
N
N
N O Cl NH
N
Alunbrig® Zejula®
N (Niraparib)
(Brigatinib)
F
HN Cl
H
N
N N
O
O N
Vizimpro® Keytruda®
(Dacomitinib) (Pembrolizumab)
FIGURE 1.3 Vizimpros (Dacomitinib) was approved in 2018 for the treatment of meta-
static non-small cell lung cancer. Zejulas (Niraparib) was approved in 2017 for the treatment
of epithelial ovarian, fallopian tube, and primary peritoneal cancers. Alunbrigs (Brigatinib)
was approved in 2017 for the treatment of metastatic non-small cell lung cancer. Keytrudas
(Pembrolizumab) was approved in 2014 for the treatment of advanced melanoma.
H2N Cl OH
O N H OH
O H O N H
H2N NH2 N O O N
S N
N N H2N
O O H2N
H2N Cl
Midamor® Lozol® Tenoretic® Inderal®
(Amiloride) (Indapamide) (Atenolol) (Propranolol)
HO
HO O
O O O OH
O HO
HS O O
O
O N O N
N H O F
N H
OH OH
O
® ® ®
Capoten Vasotec Zocor Lipitor®
(Captopril) (Enalapril) (Simvastatin) (Atorvastatin)
FIGURE 1.4 The diuretics Midamors (Amiloride) and Lozols (Indapamide), the
β-blockers Tenoretics (Atenolol) and Inderals (Propranolol), the ACE inhibitors Capotens
(Captopril), Vasotecs (Enalapril), and the HMGCoA reductase inhibitors Lipitors
(Atorvastatin) and Zocors (Simvastatin) have significantly improved the treatment of car-
diovascular disease. ACE, Angiotensin-converting enzyme.
II
During the first half of the nineteenth century the chief musical
societies in New York seem to have been the New York Choral
Society, the Philharmonic Society, the Euterpean Society, the Handel
and Haydn Society, The Musical Fund, and the Sacred Music
Society. Of the Euterpean Society we have already spoken as
having been founded probably in 1800. Apparently it was composed
chiefly of wealthy amateurs and was somewhat dilettante in its
activities. A contemporary critic thus arraigns it: 'This society, from its
long standing, the respectability of its officers, and the individual
talent of its members, might possess the most extensive influence in
the musical community. It has in its possession funds, and the
largest library of instrumental music in the country; and yet, with all
these advantages on its side, what has the Euterpean done, or what
does it do? It can be summed up in a few words. A few of its
members meet every Friday evening and play overtures and
symphonies; and every year they give an indifferent concert and a
ball, the last of which is the chief attraction. Now, we ask the
Euterpean if, like a horse in a mill, they are forever to pursue this
eternal round?'
The Euterpean did not continue that or any other course for very
long, but, whatever justice there may have been in the foregoing
criticisms, it was certainly the only instrumental music society in New
York during the years immediately preceding the advent of the
Philharmonic. Possibly its annual concert was 'indifferent,' but the
program of 1839, quoted by Dr. Ritter, which includes compositions
of Herold, Auber, Bellini, Boehm, Purcell, Rossini, and Thalberg,
would argue the contrary.[36] The orchestra was of sufficiently good
symphonic proportions. It consisted of six first violins, five second
violins, four tenors, three 'celli, two contrabasses, four flutes, two
oboes, two clarinets, two bassoons, four horns, two trumpets, three
trombones, kettle drums, drum and cymbals. Apparently the
principals in the orchestra of the Euterpean lacked zeal and
enterprise, but, whatever their faults, we are justified in looking upon
the society as the parent of the Philharmonic and as an important
factor in the development of orchestral music in New York.
The New York Choral Society, which devoted its energies to sacred
music, seems to have done very notable work during the short time it
lasted. It was founded in 1823, chiefly by Episcopal clergymen, and
its first grand concert, given at St. George's Church on Beekman
Street in 1824, is interesting enough to deserve citation:
First Part
Overture Jomelli
Air: 'Comfort ye my people,' from the 'Messiah' Handel
Chorus: Motetto, 'O God, when thou appearest' Mozart
Air: 'Thou didst not leave,' 'Messiah' Handel
Chorus: 'Lift up your hands' Handel
Duetto: 'Hear my prayer' Kent
Air: 'Oh! had I Jubal's Lyre' Handel
'Hallelujah Chorus,' from 'Mount of Olives,' Beethoven
Part Second
Four years later the Sacred Music Society produced the 'Messiah' in
its entirety, under the leadership of Uriah C. Hill, whom we shall have
occasion to meet later. There was an orchestra of thirty-eight
instruments and a chorus of seventy-four voices. Encouraged by its
success it gave Haydn's 'Te Deum' and 'Creation,' and in 1838 it
produced Mendelssohn's 'St. Paul'—only two years after that work
had made its first appearance at Düsseldorf. For reasons which we
are unable to discover the Sacred Music Society ceased to exist in
1849. Possibly the musical public of New York were not overly
inclined toward oratorio, and possibly also the society suffered from
the competition of a number of rival organizations. Most of these,
such as 'The Academy of Church Music,' were formed out of church
choirs and very evidently aspired to rival the fame of the Sacred
Music Society. None of them, however, attained any success. Their
effect, indeed, was if anything, pernicious, for what New York then
needed in its musical affairs was concentration rather than
expansion.
For a short time New York possessed a Handel and Haydn Society
which originated in a number of oratorio performances gotten up to
finance the rebuilding of the Zion Church. This was before the day of
the Sacred Music Society. The Musical Fund, already mentioned,
seems to have been chiefly an orchestral organization,
notwithstanding the fact that, as Dr. Ritter points out, it gave monthly
rehearsals for 'the display of the glee and solo talent' of the city. A
concert given by it in 1830 included the overture to Mozart's 'Magic
Flute,' an overture of Winter, a pianoforte solo, a clarinet concerto,
and a trumpet concerto(!). We find that at its concert in 1836 the
Musical Fund had a very well balanced orchestra of thirty-eight
instruments and performed, among other things, the overtures to
Rossini's 'Sémiramide' and 'William Tell.' Handel, Haydn, Mozart,
Gluck, Beethoven, Rossini, and Weber all figured on the society's
programs, and on one occasion it presented Beethoven's 'Eroica,'
arranged for septet.
III
It is quite impossible to say when and where the first musical society
made its appearance in New England. Though both Mr. Elson and
Dr. Ritter assert that the Stoughton Musical Society was founded in
1786 its right of priority is not apparent. Even if it had its beginning in
the singing school which Billings taught at Stoughton in 1774, it still
must yield precedence to the St. Cecilia and Orpheus societies of
Charleston, the Orpheus Club of Philadelphia, and the Harmonic
Society of New York—all of which were in existence before the latter
date.
How many musical societies existed in Boston during the last years
of the eighteenth century we cannot say. There seems to have been
a number of them. In 1789, during the visit of Washington to Boston,
'an Oratorio or Concert of Sacred Musick' was given in which the
choruses of the oratorio of Jonah were sung by the Independent
Musical Society. There is no evidence of the dates at which this
society began or ended its existence, but it must have been a fairly
efficient organization. There was no lack of competent musicians in
Boston at that time, and choral singing especially seems to have
been in high favor with a goodly share of the population. The society
of the Sons of Apollo, which existed in 1795, was probably a vocal
organization also, though we know nothing about it. Boston
possessed a Philharmonic Society which was founded probably
before 1799. Possibly Gottlieb Graupner, one of the most prominent
figures in the early musical life of Boston, was among its founders,
and it seems likely that it was identical with the Philharmonic Society
which is supposed to have been founded by Graupner and his
friends in 1810 or 1811. According to Mr. J. S. Dwight, author of a
'History of Music in Boston,' the Philharmonic was 'simply a social
meeting, held on Saturday evenings, when, in their small way, they
practised Haydn's symphonies.' This statement, however, does not
square with the fact that the society gave regular concerts and was
described by the musical journal, 'Euterpeiad,' as a 'useful nursery of
music.' Its last concert took place in 1824 and apparently it went out
of existence in that year.
During the last few years of the eighteenth and the first decades of
the nineteenth centuries musical societies began to spring up in the
smaller cities throughout the country. Very little information
concerning them has come to light, but it is probable that research
will finally disclose a surprising amount of serious musical activity in
places which so far have escaped mention in our musical histories.
The impression that musical culture in early America was confined to
Boston, New York, Philadelphia, and Charleston has taken firm root
and is confirmed by most of the evidence on the subject which has
appeared. But research in American musical history has for the most
part been extremely superficial and determined in its direction by
preconceived impressions which are wholly one-sided. Such special
studies in early American musical history as have been made—
those of Mr. O. G. Sonneck, for example—have exploded many
longstanding fallacies and misconceptions and undoubtedly further
research will clear the field of other myths now generally accepted as
incontestable.
W. D. D.
FOOTNOTES:
[35] Until 1790, as we have previously noted, the name was spelled 'Cæcilia.'
[36] It must not, of course, be forgotten that a comparison between this and a
modern orchestral program would be unfair. The program was light, and
conspicuously ignored the great Germans, but it was good of its time and kind. It
included an oboe solo, which must have been a novelty to New Yorkers.
CHAPTER V
THE BEGINNINGS OF OPERA
I
The first mention of theatrical performances in America is found in
the whimsical autobiography of the mercurial Tony Aston
—'Gentleman, Lawyer, Poet, Actor, Soldier, Sailor, Exciseman,
Publican; in England, Scotland, Ireland, New York, East and West
Jersey, Maryland, Virginia (on both sides Cheesapeek), North and
South Carolina, South Florida, Bahamas, Jamaica, Hispaniola, and
often a Coaster by all the same.' In the 'beginning of Queen Anne's
reign,' he tells us, he arrived at Port Royal Harbor where Governor
Moore was about to start on an expedition against St. Augustine.
This was in September, 1702. Tony accompanied Moore and
returned with him to Charleston in January, 1703. 'Well,' he says, 'we
arrived in Charles-Town, full of Lice, Shame, Poverty, Nakedness
and Hunger:—I turned Player and Poet and wrote one Play on the
Subject of the Country.' We may assume, therefore, that Charleston
witnessed theatrical performances in 1703. In the same year the
redoubtable Tony went to New York. 'There,' he says, 'I lighted of my
old Acquaintance Jack Charlton, Fencing Master, ... after acting,
writing, courting, fighting that Winter ... my kind Captain Davis ...
gave me free passage for Virginia....' Apparently, then, there were
theatrical performances in New York in the winter of 1703-04.
II
Theatrical activities were naturally curtailed severely during the war,
but with the establishment of peace there was a great revival. After
the Revolution, indeed, the popularity of the theatre became much
greater and more widespread than it ever had been before. And
coincident with the popularity of the theatre came the popularity of
opera. Even in Boston the old prejudice against the theatres began
to disappear, though the blue laws of 1750 were still in force. Several
attempts were made at various times to circumvent these laws by
presenting operas under the guise of concerts, and the resulting
performances must occasionally have been wonderfully concocted.
We find an announcement in 1770 of 'A vocal entertainment of three
acts. The songs (which are numerous) are taken from a new
celebrated opera, call'd "Lionel and Clarissa."' An entry in the diary
of John Rowe during the same year reads: 'In the evening I went to
the Concert Hall to hear Mr. Joan read the Beggar's Opera and sing
the songs.' In 1792 Alexander gave in Boston 'a musical
entertainment called the Poor Soldier delivered,' and from that time
forward the friends of opera in Boston met with no opposition, though
it was long before Boston became an operatic city.