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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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