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7
GENETIC TOXICITY: IN VITRO
APPROACHES FOR MEDICINAL
CHEMISTS
RICHARD M. WALMSLEY AND DAVID ELDER
7.1 INTRODUCTION
7.1.1 Scope of this Chapter
Positive genetic toxicitydata in preclinical developmentcan terminatethe development
path of a compound. Although this should be a very rare occurrence, at present it occurs
for 10–15% of compounds. Currently genotoxicity assessment mostly is conducted by
preclinical safetyassessmentexperts, who perform labor-intensive assays on very small
numbersof compounds. However, it is now possible to envisage a situation in which the
potentgenotoxins are identifiedbyhigh-throughputassays and evencomputerprograms
similar to other ADME/Tox liabilities. The increasing appearance of publications that
discuss genotoxicity in an earlier screening context reflects a growing willingness to
consider genotoxicity hazard assessment early in the discovery process.
This chapter explains why failure due to genotoxic hazard in safety assessment
should, and could, be reduced to 2% or lower if genotoxicity assessment were a part of
routine hit-to-lead and lead optimization screening. A basic introduction to the
fundamentals, mechanisms, and practices of genetic toxicology is provided, along
with brief descriptions of the regulatory GLP assays and the newer pre-GLP screening
methods. The chemistry of genotoxins and the use of in silico methods for the
prediction of genotoxicity are reviewed. Some examples of approaches to genotoxicity issues are provided. Finally, the current guidelines for regulatory genotoxicity
ADMET for Medicinal Chemists: A Practical Guide, Edited by Katya Tsaioun and Steven A. Kates
Copyright 2011 John Wiley & Sons, Inc.
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assessment are discussed along with the prospects for change in the future, and how
these might affect screening strategies.
7.1.2 Definitions
For the purposes of this chapter, genotoxins are defined as agents that cause genome
damage. This damage includes all quantifiable changes in DNA base sequence
(mutagenesis), chromosome number (aneugenesis), and chromosome content (translocation) as well as single- and double-strand DNA breaks (clastogenesis). Direct
damage to DNA may be caused by a compound, or its metabolic product, reacting or
interacting with DNA, either to form adducts or through subsequent processing to
alter a DNA base, etc. Indirect damage is a consequence of interference with either the
enzymes associated with DNA replication and repair, or with the ordered segregation
of chromosomes during mitosis. The term “indirect damage” can also appl y to
processes which lead to the generation of reactive oxygen species, which can
damage DNA. Some authors use the term “indirect acting agents,” to describe
promutagens/progenotoxins—compounds which become genotoxins following metabolism—but for this chapter the former is used. To detect these many different types
of DNA/genome damage, a variety of methods have evolved. In this chapter, these will
be considered in terms of their utility as early screening methods.
Early in the development of this field, there was an assumption that if a compound
was a carcinogen, then any dose would pose a hazard. However, it h as become clear
that for some compounds there is a threshold dose, up to which there is no hazard. This
is particularly important in the assessment of pharmaceutical safety. If a compound is
pharmacologically active at a very low dose, but has been shown to carry a genotoxic
liability threshold, it might be argued successfully that the intended dose and exposure
for the patient are acceptable.
Sensitivity, specificity, and concordance are the terms most frequently used to
define the performance of the genotoxicity assays. Sensitivity is defined as the
proportion of in vivo genotoxins or genotoxic carcinogens, which give a positive
result in an assay. Specificity is defined as the proportion of noncarcinogens, which
give a negative result in an assay. Con cordance is defined as the overall proportion of
correct positive and negative results obtained. In order to compare figures for
concordance between different assays, there should either be approximately equal
numbers of positive and negative compounds in the studies, or results from the same
collection should be compared.
7.1.3 Positive Genotoxicity Data is not Uncommon and Very Costly
A recent study reported that serious safety concerns arise from genotoxicity in about
15% of drug candidates [1]. Such compounds might be abandoned, writing off the
huge expenses of discovery and early development. However, the prevalence of
misleading positive in vitro genotoxicity results, discussed later in this chapter,
indicates that compounds with positive data can often be taken safely to market
providing that there is an adequate risk-benefit balance for the patient. The costs of
additional animal studies that might assure human safety are dwarfed by the costs of
delayed clinical trials —and even these costs become insignificant, compared with the
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loss of revenue from delays to market. The extent of these problems is reflected in the
US Physicians Desk Reference [2], where about 25% of compounds have adverse
genotoxicity labeling [3]. These have been taken to market for nonlife threatening
therapies because the observed genotoxicity was not found to present hazard to
humans. These include Acyclovir (over the counter antiviral), Citalopram (antidepressant), Claritin (over the counter antiallergy), Griseofulvin (antifungal), theophylline (bronchodilator), and Zolmitriptan (antimigraine medicine). There are currently efforts from many international agencies to address the “false positive”
problem and these issues are also addressed in this chapter.
7.1.4 Why Genome Damage is Undesirable
The genome stores information encoded by DNA. Compounds which cause corruption in either the information itself or the control of its use can lead to serious illnesses
including cancer and inherited susceptibility to illness. Genetic toxicologists are
concerned with the identification of such genotoxic compounds and the mechanism
by which they exert their effects. In general, and in this chapter, the focus is on those
compounds that either directly or indirectly causes alteration to the genome sequence
and organization. There are also semipermanent changes in gene expression, which
can be linked to local changes in the normal patterns of DNA and histone modification, as well as epigenetic changes, or the expression of interfering microRNA
molecules. Compounds that affect such changes are often nongenotoxic carcinogens.
This latter class is less well understood and is currently not part of the genetic
toxicologist’s domain. The reader is referred to a recent review [4].
7.1.5 The Inherent Integrity of the Genome and its Inevitable Corruption
During physiological development, information in the genome is used to control cell
division and differentiation into different tissue/cell types. This differentiation is a
consequence of the selective activation and inactivation of genes. Selective cell
killing/suicide or apoptosis is also programmed part of development, and occurs
during such diverse processes as neuron development and the separation of fingers and
toes. However, apoptosis is also part of the evolved response to overwhelming DNA
damage. This is perhaps the most extreme, but most effective limitation to the
potentially harmful overaccumulation of mutations during the natural life span.
There are some evolved exceptions to conservation of sequence. These exceptions
are found within the cells of the immune system, the germ cells of the ovary and testis,
and at the telomeres, the ends of the chromosomes. Cells in the immune system have
evolved to deliberately shuffle subsets of information, generating diversity in the
antibodies that protect the body from a variety of exogenous agents. During meiosis,
the germ cells make different combinations of the diverse maternal and paternal genes
that came together in the individual. This process allows the segregation of genuinely
new information sets, and hence diversity in subsequent generations. The ends of
chromosomal DNA molecules are protected by the repetitive DNA sequences of the
telomere and their associated proteins. Telomeres shorten with age, and eventually
lose their protective properties. This leads to cell death, which contributes critically to
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the aging process. At approximately 52 sequential cell divisions, most cells lose the
ability to divide further.
During active cell division, individual cells will steadily accumulate random
mutations. These will arise from the rare errors in DNA replication prior to cell
division, as well from the oxidative DNA damage caused by the reactive oxygen
species generated by the depend ence on oxidative metabolism. These are unavoidable
hazards which contribute to the overall risk of cancer. Toxin-induced cell damage and
cell death lead to extra cell divisions to replace lost tissue, so repeated or long-term
exposure to a variety of poisons leads to increased accumulation of random mutations
caused by increased cell division. The longer a human lives, the more errors
accumulate, and the increased likelihood of corrupting the genes which ensure that
proper cell division occurs. This is part of the reason for the increased incidence of
tumors found in populations as the average age at death increases. There is essentially
no selection against age-related diseases that emerge postreproductively.
7.1.6 Many Chemicals can Cause Cancer, but do not Pose a Significant Risk
to Humans
There are a few well-known and often avoidable genotoxic hazards. For example,
ionizing radiation and ultraviolet radiation both increase the incidence of genome
damage and tumorigenesis. However, there are countless less well-known hazards,
including the almost countless xenobiotics that humans inhale, eat, and drink. It is not
uncommon to read of the genotoxicity of common food from bread and chips (French
fries) to barbequed meat. It has been estimated that a human consumes gram quantities
of genotoxins every day [5], though as with any potential poison, the actual risk is a
function of dose/exposure. The carcinogenicity potency data base [6] shows that
nearly 70% of all natural and synthetic compounds that have been tested are rodent
carcinogens. However, for most of these compounds, it would be difficult for a human
to consume the same dose that caused tumors in the rodents. For many, the additional
cell divisions caused by high toxic doses in early LD
50
studies were presumably the
reason for the observed tumors rather than genotoxic effects.
7.1.7 The False Positives: Many Chemicals Produce Positive Genotoxicity
Data that are neither Carcinogens nor In Vivo Genotoxins
Most of the current in vitro mammalian assays were developed for late-stage safety
assessment, with full appreciation of the limitations in nonanimal systems. For many
years there was an emphasis on developing high sensitivity without corresponding
attention to specificity. The result has been the establishment of tests generating a high
prevalence of positive data, within collections of noncarcinogens as well as carcinogens. As previously noted, about 25% of pharmaceuticals in Physicians Desk
Reference, registered for use with clinical indications, excluding antineoplastic and
antiviral drugs, have positive data from in vitro mammalian genotoxicity tests. The
positive results were concluded not to be relevant to humans. Subsequent studies of
data from both drug submissions [7] and other chemicals in the public domain [8]
318 GENETIC TOXICITY: IN VITRO APPROACHES FOR MEDICINAL CHEMISTS
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