Defining targets for investigating the pharmacogenomics of adverse drug reactions to antifungal agents

Adverse drug reactions (ADRs) associated with antifungal therapy are major problems in patients with invasive fungal infections. Whether by clinical history or patterns of genetic variation, the identification of patients at risk for ADRs should result in improved outcomes while minimizing deleterious side effects. A major contributing factor to ADRs with antifungal agents relates to drug distribution, metabolism and excretion. Genetic variation in key genes can alter the structure and expression of genes and gene products (e.g., proteins). Thus far, the effort has focused on identifying polymorphisms with either empirical or predicted in silico functional consequences; the best candidate genes encode phase I and II drug-metabolizing enzymes (e.g., CYP2C19 and N-acetyltransferase), plasma proteins (albumin and lipoproteins) and drug transporters (P-glycoprotein and multidrug resistance proteins), which can affect the disposition of antifungal agents, eventually leading to dose-dependent (type A) toxicity. Less is known regarding the key genes that interact with antifungal agents, resulting in idiosyncratic (type B) ADRs. The possible role of certain gene products and genetic polymorphisms in the toxicities of antifungal agents are discussed in this review. The preliminary data address the following: low-density lipoproteins and cholesteryl ester transfer protein in amphotericin B renal toxicity; toll-like receptor 1 and 2 in amphotericin B infusion-related ADRs; phosphodiesterase 6 in voriconazole visual adverse events; flavin-containing monooxygenase, glutathione transferases and multidrug resistance proteins 1 and 2 in ketoconazole and terbinafine hepatotoxicity; CYP enzymes and P-glycoprotein in drug interactions between azoles and coadministered medications; multidrug resistance proteins 8 and 9 on 5-flucytosine bone marrow toxicity; and mast cell activation in caspofungin histamine release. This will focus on high-priority candidate genes, which could provide a starting point for molecular studies to elucidate the potential mechanisms for understanding toxicity associated with antifungal drugs as well as identifying candidate genes for large population prospective genetic association studies.     

Association of candidate genes with antisocial drug dependence in adolescents

The Colorado Center For Antisocial Drug Dependence (CADD) is using several research designs and strategies in its study of the genetic basis for antisocial drug dependence in adolescents. This study reports single nucleotide polymorphism (SNP) association results from a targeted gene assay (SNP chip) of 231 primarily Caucasian male probands in treatment with antisocial drug dependence and a matched set of community controls. The SNP chip was designed to assay 1500 SNPs distributed across 50 candidate genes that have had associations with substance use disorders and conduct disorder. There was an average gene-wide inter-SNP interval of 3000 base pairs. After eliminating SNPs with poor signals and low minor allele frequencies, 60 nominally significant associations were found among the remaining 1073 SNPs in 18 of 49 candidate genes. Although none of the SNPs achieved genome-wide association significance levels (defined as p<.000001), two genes probed with multiple SNPs (OPRM1 and CHRNA2) emerged as plausible candidates for a role in antisocial drug dependence after gene-based permutation tests. The custom-designed SNP chip served as an effective and flexible platform for rapid interrogation of a large number of plausible candidate genes.     

Chemical genomics and emerging DNA technologies in the identification of drug mechanisms and drug targets

Chemical genomics combines chemistry with molecular biology as a means of exploring the function of unknown proteins or identifying the proteins responsible for a particular phenotype induced by a small cell-permeable bioactive molecule. Chemical genomics therefore has the potential to identify and validate therapeutic targets and to discover drug candidates for rapidly and effectively generating new interventions for human diseases. The recent emergence of genomic technologies and their application on genetically tractable model organisms like Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae have provided momentum to cell biological and biomedical research, particularly in the functional characterization of gene functions and the identification of novel drug targets. We therefore anticipate that chemical genomics and the vast development of genomic technologies will play critical roles in the genomic age of biological research and drug discovery. In the present review we discuss how simple biological model organisms can be used as screening platforms in combination with emerging genomic technologies to advance the identification of potential drugs and their molecular mechanisms of action.     

Structural pharmacogenomics,drug resistance and the design of anti-infective super-drugs

Large-scale comparative analysis of drug-target polymorphism structures enables the rational design of next generation ‘super drugs’ – drugs that are less prone to development of drug resistance or that work for the largest possible fraction of the patient population. Furthermore, knowledge of the drug-target-shape repertoire that exists within the patient population enables predictions of likely clinical trial outcomes and response rates for drug efficacy. This gives information on the optimal drug candidates before the initiation of clinical trials. The economic impact of incorporating pharmacogenomics insights early on in the drug discovery process will be substantial and will afford significant competitive advantages to companies that successfully incorporate this technology.     

药物基因组学在药物研发中的转化与应用

药物安全性和有效性是新药开发和临床用药的核心问题,也是药物基因组学研究的主要内容。目前,已阐明影响药物安全性有效性及个体化差异的首要因素是药物相关生物标记。近年来,药物基因组学各机构正式成立,各发达国家也纷纷出台各种规章,对药物研发中药物基因组学的应用进行规定。药物基因组学在上市药物的评价中已获得巨大的成功,并成功指导了数例肿瘤靶向药物从研发到上市的全过程,缩短了药物开发周期、降低了研究成本及毒副反应。     

Role of pharmacogenomics in drug discovery and development

Pharmacogenetics and pharmacogenomics are two major emerging trends in medical sciences, which influence the success of drug development and therapeutics. In current times, though pharmacogenetic studies are being done extensively for research, its application for drug development needs to get started on a large scale. The major determinants of success of a new drug compound, viz safety and efficacy, have become more predictable, with the advent of pharmacogenetic studies. There is a need felt for pharmacogenomic studies, where the effects of multiple genes are assessed with the study of entire genome.Pharmacogenetic studies can be used at various stages of drug development. The effect of drug target polymorphisms on drug response can be assessed and identified. In clinical studies, pharmacogenetic tests can be used for stratification of patients based on their genotype, which corresponds to their metabolizing capacity. This prevents the occurrence of severe adverse drug reactions and helps in better outcome of clinical trials. This can also reduce attrition of drug compounds. Further, the variations in drug response can be better studied with the wider application of pharmacogenomic methods like genome wide scans, haplotype analysis and candidate gene approaches. The cost of pharmacogenetic testing has become very low, with the advent of newer high throughput genotyping systems. However, the cost of pharmacogenomic methods continues to be very high. As the treatment with several drugs is being more and more pharmacogeneticaly guided (e.g. warfarin and irinotecan), the FDA has laid down guidelines for pharmaceutical firms regarding submission of pharmacogenetic data for their drug products in labelling.     

Drugs, their targets and the nature and number of drug targets

What is a drug target? And how many such targets are there? Here, we consider the nature of drug targets, and by classifying known drug substances on the basis of the discussed principles we provide an estimation of the total number of current drug targets.     

Estimating the contribution of genes and environment to variation in renal drug clearance

Renal excretion is the major pathway for elimination of many clinically used drugs and xenobiotics. We estimated the genetic component (rGC) contributing to variation in renal clearance for six compounds (amoxicillin, ampicillin, metformin, terodiline, digoxin and iohexol) using Repeated Drug Application methodology. Data were obtained from published literature. The rGC values of renal clearance of metformin, amoxicillin, and ampicillin, which undergo transporter-mediated secretion, ranged from 0.64-0.94. This finding suggests that variation in the renal clearance of these drugs has a strong genetic component. Additionally, the rGC values of renal clearance of metformin, amoxicillin, and ampicillin were similar to previously reported rGC values for metabolism. By contrast, the rGC values of renal clearance for iohexol, digoxin, and terodiline were low (0.12-0.37). Renal clearance of these compounds occurs mainly through passive processes (e.g. glomerular filtration and passive secretion/reabsorption). The low rGC values of iohexol, digoxin and terodiline suggest that environmental factors may contribute to variation in their renal clearance.     

Human kinome drug discovery and the emerging importance of atypical allosteric inhibitors

Importance of the field: Protein kinases are important targets for drug discovery because they possess critical roles in many human diseases. Several protein kinase inhibitors have entered clinical development with others having already been approved for treating a host of diseases. However, many kinase inhibitors suffer from non-selectivity because they interact with the ATP binding region which has similar structures amongst the protein kinases and this non-selectivity sometimes can cause side effects. As a consequence, there is much interest in developing drugs that inhibit kinases through non-classical mechanisms with the hope of avoiding the side effects of previous kinase drugs. Areas covered in this review: This review covers emerging information on kinase biology and discusses new approaches to design selective inhibitors that do not compete with ATP. What the reader will gain: The reader will gain a better understanding of the importance of the field of allosteric inhibitor drug discovery and how this has required the adoption of a new generation of high-throughput screening techniques. Take home message: Discovery and development of allosteric modulators will result in a family of novel kinase therapies with greater selectivity and more varied ways to control activity of disease causing kinase targets.     

The sequence specificity of the anti-tumour drug, cisplatin, in telomeric DNA sequences compared with consecutive guanine DNA sequences

The sequence specificity of the anti-tumour drug, cisplatin, was determined in a DNA sequence that contained seven telomeric repeats and a run of ten consecutive guanine bases. Cisplatin preferentially forms DNA adducts at consecutive guanine sequences. Hence these DNA sequences were examined in order to gain an insight into the important human genomic regions that are damaged by cisplatin. A polymerase stop/linear amplification assay was employed with an automated DNA capillary sequencer and laser-induced fluorescence detection to quantitatively determine the DNA sequence specificity of cisplatin in a plasmid clone containing seven telomeric repeats and a sequence of ten consecutive guanine bases. It was found that cisplatin preferentially damaged the ten consecutive guanine sequence although the telomeric DNA sequences were also a major site of cisplatin adduct formation.     

Applying pharmacogenomics to enhance the use of biomarkers for drug effect and drug safety

Pharmacogenomics is used to improve patient outcome by maximizing the likelihood of desired effects and minimizing the risk of adverse events using an individual's genetic profile. As such, pharmacogenomics can be used to improve current risk-management strategies (improving the risk-benefit balance). Two areas of great promise for pharmacogenomics in this regard are emerging: (i) the pharmacogenomics of modulating disease biomarkers (to provide insight into novel mechanisms of drug response and to identify the patients most likely to respond to a drug in a favorable way); and (ii) using pharmacogenomics to enhance drug safety. Given that novel biomarkers could enable the earlier detection of many diseases and more-widespread therapies for primary prevention, pharmacogenomics provides the opportunity to identify the patients most likely to respond to these therapies, thereby preserving valuable health-care resources. The use of pharmacogenomics in pharmacovigilance could also be useful for risk-stratifying patients and for helping to identify the mechanisms involved in adverse events.     

Clinical applicability of sequence variations in genes related to drug metabolism

The Human Genome and the Hap Map Projects as well as the extensive use of deep resequencing worldwide, have contributed to a massive catalogue of reported single nucleotide polymorphisms (SNPs) and other genetic variations in the human genome. Pharmacogenomics is an emerging field that combines genetics with pharmacokinetics and pharmacodynamics of the drug in attempt to understand inter-individual differences among patients and develop more accurate drug dosing. However, only for the minority of those variations an association with phenotype has been established. Here, we provide an overview of genes and genetic variants that influence inter-individual dosing of three of the most widely used drugs, namely warfarin, irinotecan and thiopurine drugs, to highlight a tangible benefit of translating genomic knowledge into clinical practice. Therefore, particular SNPs in vitamin K epoxide reductase complex subunit 1 (VKORC1), cytochrome P450 2C9 (CYP2C9), uridine diphosphate glucoronosyltransferase 1A1 (UGT1A1) and thiopurine S-methyltransferase (TPMT) genes has proven to be applicable for optimising the dosage in pursuit of maximum efficacy and minimum adverse effects. Thus, they set an important paradigm of implementation of pharmacogenomics in the mainstream clinical practice.     

The role of common variation in drug transporter genes in refractory epilepsy

Resistance to antiepileptic drugs (AEDs) is one of the most serious clinical problems in epilepsy, and along with AED teratogenicity, perhaps the major concern of epilepsy pharmacogenetics. Studying the genetics of drug resistance in epilepsy is important, as it may identify or confirm key mechanisms underlying this phenomenon that have real clinical importance; it might also offer insights into its prediction and management. Drug resistance in epilepsy is likely to be multifactorial: overactivity of multi-drug transporters provides one likely underlying mechanism through lowering of AED concentration in the epileptogenic focus. Genetic association studies may provide a tool to assess this 'transporter' hypothesis by determining whether differences between individuals contribute to resistance phenotypes. Most of these studies have investigated one variant in the ABCB1 gene, and have provided, thus far, inconclusive evidence. This review also considers current knowledge of the role of genetic polymorphisms in multi-drug transporters in pharmacoresistant epilepsy, to highlight possible confounding factors affecting the implementation and interpretation of association studies in this field.     

Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes

Genetic variations have been associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification and pharmacogenetics. Commonly used gel electrophoresis-based genotyping methods for known polymorphisms include polymerase chain reaction (PCR) coupled with restriction fragment-length polymorphism analysis, allele-specific amplification, and oligonucleotide ligation assay. Fluorescent dye-based DNA fragmentation has been extensively used for high-throughput microsatellite or short tandem-repeat genotyping. TaqMan and molecular beacon genotyping are commonly used homogeneous solution hybridization technologies. Because of the ease of experimental assay design, single nucleotide polymorphism (SNP) genotyping methods based on single-base extension are in rapid development, such as fluorescence homogenous assays, pyrosequencing and mass spectrometry. Non-PCR based genotyping assays such as Invader trade mark assays are promised to genotype directly from genomic DNA without the requirement of PCR amplification. The DNA microarray is a solid phase genotyping format that is rapidly developing for parallel genotyping of a large number of SNPs simultaneously. Advanced technologies to identify genetic polymorphisms rapidly, accurately, and cost effectively will fundamentally change the practice of medicine by allowing physicians to prescribe medicine based on a patient's genetic make-up.     

Prediction of concentration-time profile and its inter-individual variability following the dermal drug absorption

Estimation of systemic exposure after absorption of any xenobiotic from the skin is very important in development of dermal pharmaceutical products as well as assessing un-intended exposures due to cosmetic products or environmental and occupational compounds. Historically, animal models have been used to evaluate dermal drug absorption before conducting human trials. However, occasional disparity between the animal and human data plus rising public interest and regulatory requirements to reduce animal usage in research combined with high cost and time-consuming attributes of animal experiments have prompted many academic and industrial researchers to develop economically viable and scientifically robust in silico and in vitro methods to assess dermal drug absorption. There are a number of in silico models available in literature from quantitative structure-activity relationship to semi-mechanistic to physiologically based mechanistic models. Nonetheless, to the best of our knowledge, so far, there has been no attempt to combine mechanistic skin absorption model with database of physiological variability to simulate the inter- and intra-individual variability observed in human trials. Thus, we report here mechanistic dermal absorption model with formulation, stratum corneum, viable epidermis-dermis and blood compartments along with datab"ase of human dermal physiological variability including gender, ethnic and site of application variations. The developed model is incorporated into the Simcyp simulator which is a 'bottom-up' platform and database for mechanistic modelling and simulation of the drug disposition process using full body physiologically based pharmacokinetics model. The built model is validated using the clinical pharmacokinetic data from five different topical formulations of diclofenac. The effect of penetration enhancers, site of application, gender and ethnic variations were incorporated to simulate the clinical trials. The applied mechanistic dermal absorption model when combined with skin physiological database was able to recover well the observed clinical pharmacokinetics and population variability in all the five validation studies.