The role of genomics in the development of new and improved therapies

Transcription

1 The role of genomics in the development of new and improved therapies An appreciation of the importance of genetic diversity will have a profound impact on how drugs are discovered, developed and prescribed. Dr Roy Pettipher, Oxagen Ltd The pace of drug discovery will be greatly accelerated by The Human Genome Project and other initiatives to sequence all three billion base pairs of the human genome. The first phase of this project - completion of the sequence and mapping of all human genes - is set for completion by 2003, with a first draft becoming available in the near future. Amongst many other scientific opportunities, this will present us with a list of all possible drug targets. Unfortunately, however, these valuable entities will be scattered amongst the 120,000 genes we expect to find. The challenge will be to find the small percentage of genes encoding proteins that are both tractable drug targets, and that influence disease susceptibility or are involved in pathological processes. An understanding of how genetic diversity underlies disease will be crucial to selecting such targets on a rational basis. Genetic diversity, including individual risk of disease, is largely defined by the occurrence of single nucleotide polymorphisms (SNPs) within genes. Most SNPs probably have little or no effect on gene expression or protein activity. Of critical importance in determining risk of disease are the rarer functional SNPs that affect gene expression, alternative splicing patterns and the catalytic activity or binding properties of the gene product. It is the combination of functional polymorphisms in a number of key genes - perhaps as few as a thousand - interacting with environmental factors, that determine both the risk of developing common diseases and how patients will respond to treatment. 62 Innovations in Pharmaceutical Technology

2 Using genetics to improve medicine Despite the dramatic advances in healthcare over the last century, a number of serious diseases - including cancer, heart disease, arthritis, osteoporosis, Alzheimer s diseases and asthma - remain poorly treated. Current therapies are often only effective in treating the symptoms of established disease, and vary dramatically in efficacy and side effects among individuals. It is thought that around 30 per cent of patients do not respond satisfactorily to the most common classes of prescription drugs, such as antidepressants (both tricyclics and selective serotonin re-uptake inhibitors), β2 agonist bronchodilators, β-blockers, ACE inhibitors, anti-migraine drugs and others. Variable response rates combined with the high costs of certain new drugs, particularly biological agents, have resulted in certain healthcare providers refusing to pay for treatment with these agents, thus denying potentially responsive populations of patients access to effective treatments for serious conditions such as cancer and multiple sclerosis. It is also becoming increasingly appreciated that drug-related toxicity is a significant cost to society. It has been estimated that 6.7 per cent of US prescriptions in 1994 resulted in serious adverse reactions, the fifth leading cause of death for that year (1). Since so many patients do not respond satisfactorily to current drug therapies, the inescapable conclusion is that many patients are exposed to the risk of serious toxic side effects without any potential benefit. Consequently there is a pressing need to discover better medicines that have a more profound impact on disease processes, and also to target those drugs to patients who will derive the most benefit without the risk of serious side effects. Understanding the genetic basis of disease is likely to provide novel approaches to allow more effective treatment of established disease, but will also ultimately provide fundamental insights that may facilitate the prediction and prevention of these conditions. Most genomics-based target discovery programmes within the pharmaceutical industry have, to date, focused on mining of genomic databases to identify novel members of known drug target families, and the transcriptional analysis of such genes in various tissues throughout the body. The goal of such research is to identify tractable molecular targets that are differentially expressed in diseased tissues but are absent in other tissues throughout the body - the assumption being that drugs interacting with such a target will have a significant therapeutic impact on disease with minimal mechanism-based side effects. Sequencing of the human genome will expedite this gene discovery process and will undoubtedly yield a plethora of potential drug targets. However, differential expression of a candidate gene does not mean that this molecular target is causally linked to disease - it could be merely a consequence of the disease process. Furthermore, attractive drug targets may not necessarily be over-expressed in diseased tissue - the activity of many molecular targets, such as ion channels and G-protein coupled receptors, are not regulated at the level of gene or protein expression and do not demonstrate an enhanced expression in disease. Potential drug targets identified by differential gene expression must be validated to increase confidence that a drug that interferes with that pathway will be effective. Such validation can be provided through knock-out studies in mice, or through the activity of inhibitors (antibodies or small molecules) in animal models that are designed to mimic human disease. This process is time-consuming and unlikely to provide a practical solution to the problem of validating and prioritising the vast number of potential drug targets that are emerging from genomic studies. As the sequencing of the human genome nears completion, genetic studies will play an increasingly important role in validating new molecular targets identified through differential expression. Figure 1 illustrates how understanding the genetic basis of disease enriches the knowledge gained through genomics. Genetic validation of drug targets To understand how genetic studies can be used to validate and prioritise drug targets, it is important to appreciate that polymorphism in genes is common and that such polymorphisms can contribute towards the development of disease. It is now thought that an SNP occurs every base pairs (at a frequency of at least 5 per cent in the population) and, on average, each gene contains one functional SNP in its coding region that is predicted to change the structure, and possibly function, of the gene product (2). A gene may also have SNPs in its promoter region that may affect the level of expression in tissues throughout the body, while SNPs in intronic regions may control alternative splicing of mrna. It is these alternative forms of genes or alleles that, in combination with other genetic or environmental risk factors, trigger the onset of disease. For example, it is easy to imagine how a polymorphism in an endogenous protease inhibitor or regulatory cytokine that reduced function could, in combination with other factors, predispose individuals to diseases such as arthritis where cytokine-driven protease production plays a central role in pathology. If a drug target could be shown to be a genetic risk factor for disease, this would provide much sought-after validation of that approach. Drugs Genetic diversity, including individual risk of disease, is largely defined by the occurrence of single nucleotide polymorphisms (SNPs) within genes Innovations in Pharmaceutical Technology 63

3 Figure 1. Illustration of how the interaction between an individual s genetic make-up and environmental factors can precipitate pathology leading to disease symptoms. Knowledge of the genetic basis of disease enriches information gained from the study of the biochemistry of disease and differential gene expression. Figure 2. Some drug targets may be genetic risk factors that predispose to disease. Identification of such targets, that are likely to be linked to a critical disease pathway, will ultimately lead to the discovery and development of drugs with improved therapeutic benefit. 64 Innovations in Pharmaceutical Technology

4 ... differential expression of a candidate gene does not mean that this molecular target is causally linked to disease... Genetics also offers opportunities to ensure that... trials are streamlined in order to get promising new medicines to the market more quickly targeted to this pathway are much more likely to show significant therapeutic activity. This is an important consideration - around 50 per cent of candidate drugs fail in late stage clinical trials due to lack of efficacy. Advancing drug candidates that interfere with a pathway known to be linked to disease is, therefore, likely to significantly reduce the attrition rates that increase the cost of pharmaceutical development. As illustrated in Figure 2, not all genetic risk factors are suitable drug targets - but identification of the small proportion of drug targets that are also risk factors will allow the selection and prioritisation of the most promising approaches. There are already a few examples where genetic studies have highlighted a drug target linked to an important disease pathway. In some cases, the findings are unexpected - such as when the ALIVE study demonstrated that certain individuals who were resistant to HIV infection carried a loss-offunction mutation in the chemokine receptor, CCR-5 (3). This led to the discovery that CCR-5 is a co-receptor for the AIDS virus, and highlighted an exciting approach to prevent AIDS infection. More recently, germ-line loss-of-function mutations in PPAR-γ - a target for the action of the glitazone class of antidiabetic drugs - have been shown to cause a rare form of type 2 diabetes (4). It is quite possible that more common (and more subtle) polymorphisms in PPAR-γ could contribute to insulin resistance in more common forms of type 2 diabetes. Detection of the common alleles with lower individual relative risk will require larger genetic studies involving the collection of DNA samples from probands, affected siblings and parents so that the inheritance patterns of disease-causing alleles can be defined. Gathering such family collection materials in a number of common diseases requires a considerable investment but, once established, they provide an invaluable resource for target validation. Using genetics in clinical trials The choice of higher quality drug targets is essential to improve productivity rates in drug development. However, it is also important that candidate drugs are evaluated properly in clinical trials to maximise their therapeutic potential. Genetics also offers opportunities to ensure that these trials are streamlined in order to get promising new medicines to the market more quickly. As knowledge of the genetic basis of disease and drug responsiveness grows, a number of genetic markers are emerging that predict the degree of therapeutic efficacy or side effects for a number of classes of drug. In asthmatic patients, polymorphisms in the β2-adrenoceptor predict responses to inhaled β2-agonists (5), while individuals who carry a particular polymorphism in the 5-lipoxygenase gene (ALOX5) do not respond to 5-lipoxygenase inhibitors (6). In other therapeutic areas, including CNS disorders and cardiovascular diseases, there are numerous reports of pharmacogenetic markers that influence drug responsiveness. These are often drug targets or associated genes, but in some cases these markers are often risk factors that are not directly linked to the drug response pathway. This is the case for the apolipoprotein E4 allele, the presence of which predicts lack of cognitive response to cholinesterase inhibitors, as well as being a risk factor for Alzheimer s disease (7). Mechanism-related side effects are often more prevalent in individuals with particular genotypes or haplotypes. An example of this is the risk of Parkinson s disease patients developing levodopa-induced dyskinesia side effects - an effect that correlates with polymorphisms in the dopamine D 2 receptor (8). In addition to the documented clinical examples discussed above, many drug candidates in pre-clinical development are known to exert their effects through polymorphic receptors or enzymes. This genetic diversity must be taken into account when conducting clinical trials, since functional polymorphisms in these targets are likely to affect drug potency and/or the incidence of adverse reactions. Consequently, placebo and dose groups should be balanced for the presence of different variants to minimise the impact of variability in drug response. This information can be used later to stratify clinical trial populations, and identify those patients who derived therapeutic benefit without side effects. To perform pharmacogenomic stratification in clinical trials, it is of course necessary to collect DNA samples from the enrolled patients. It is now becoming routine practice for the leading pharmaceutical companies to collect DNA samples from participants in Phase III trials. As well as affecting the pharmacodynamic profile of a drug, genetic diversity can have a profound influence on how a drug is metabolised. Many of the enzymes involved in absorption, distribution, metabolism and elimination (ADME) are known to be polymorphic. This is particularly true of the cytochrome P450 (CYP) enzymes that are involved in Phase I oxidative reactions in the liver. The most important polymorphic drugmetabolising enzyme discovered to date is CYP2D6, which is involved in the metabolism of over 25 per cent of marketed drugs. Inheritance of two copies of a defective CYP2D6 gene leads to a poor metaboliser phenotype, a condition seen in around 7 per cent of Caucasians that has been shown to have a detrimental clinical impact under a number of circumstances. Furthermore, some individuals inherit multiple copies of this gene leading to an ultra-fast metabolic phenotype, where 66 Innovations in Pharmaceutical Technology

5 the drug is metabolised too rapidly to exert a significant pharmacological effect. Conducting pharmacokinetic studies in well-characterised, poor metabolisers is a sensible way to determine if a compound has metabolic liabilities that could precipitate an adverse reaction due to build-up of parent drug or toxic metabolites generated through an alternative pathway. These studies need to be conducted early in the clinical development process to avoid problems emerging in later development when a heavy investment has already been made. If it is suspected that a compound is a substrate for CYP2D6, or other polymorphic enzymes associated with variable metabolism, it is likely that regulatory authorities will demand pharmacokinetic studies in poor metabolisers prior to approval. Conclusion It is becoming increasingly apparent that the exponential growth in knowledge of gene sequence and function has the potential to transform healthcare. It is ultimately the appreciation of the importance of genetic diversity that will have a profound impact on how drugs are discovered and how they are prescribed. Genomic technologies can be used to identify new genetically validated targets, which will make the drugs of the future safer and much more effective than the current treatments available for heart disease, degenerative disease and cancer. Applying genetics to clinical trial design can reduce the risk of compound failure, and ensure that the drugs are targeted to the right patient. Understanding the genetic basis of disease will shift the focus of healthcare from detection and treatment towards prediction and prevention of serious illnesses. Dr Roy Pettipher joined Oxagen in Previously, he worked at Pfizer in the US where he was involved in the initiation and management of a number of research programmes to identify drug candidates that inhibit the production of cytokines and other mediators involved in inflammatory disease. Dr Pettipher studied for his PhD at The Wellcome Research Laboratories in the UK on the role of cytokines and proteases in cartilage degradation and other aspects of chronic arthritis. He holds a PhD from the University of London and an MBA from Imperial College. References 1. Lazarou J, Pomeranz BH, Corey PN (1998). Incidence of adverse drug reactions in hospitalized patients. A meta-analysis of prospective studies. JAMA, 279, Cargill M et al. (1999). Characterization of single nucleotide polymorphisms in coding regions of human genes. Nature Genetics, 22, Dean M et al. (1996). Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science, 273, Barroso I et al. (1999). Dominant negative mutations in human PPARg associated with severe insulin resistance, diabetes mellitus and hypertension. Nature, 402, Lima JJ et al. (1999). Impact of genetic polymorphisms of the b2-adrenergic receptor on albuterol bronchodilator pharmacodynamics. Clin Pharmacol Ther, 65, Drazen JM et al. (1999). Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment. Nature Genetics, 22, Poirier J et al. (1995). Apolipoprotein E4 allele as a predictor of cholinergic deficits and treatment outcome in Alzheimer disease. Proc Natl Acad Sci, 92, Oliveri RL et al. (1999). Dopamine D2 receptor gene polymorphism and the risk of levodopa-induced dyskinesias in PD. Neurology, 53, As well as affecting the pharmacodynamic profile of a drug, genetic diversity can have a profound influence on how a drug is metabolised Innovations in Pharmaceutical Technology 67