Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919), страница 93
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The majority of our current therapeutic armamentarium developed during this era. Advances in the fields of molecular biologyand genetics brought forth a new era in drug discovery at the turn of the new millennium. As a result, genomics, proteomics, and bio-informatics are used in complementation with the modern tools of chemistry and pharmacology to designand develop new drugs.Genomics, defined as information derived from the structure and organizationof the genes of an organism, are used to identify targets, validate targets and leadcompounds and to individualize therapy.
Advances in genomics in conjunctionwith the modern techniques of combinatorial chemistry and high-throughputscreening have provided an unprecedented wealth of information for efficient andless costly drug discovery. Various genomic-based techniques, such as highthroughput DNA and protein sequencing, DNA microarray chips for expressionprofiling, mass spectrometry, and bio-informatics have been developed and usedto identify and validate targets for pharmacological interventions.
In parallel withthese efforts, a complementary phase of genomic research has already begun withthe goal of identification and construction of single nucleotide polymorphism(SNP) and haplotype maps of the human genome. The ultimate goals are to mapand identify the susceptibility genes for common complex diseases in order to develop new therapeutic targets and to individualize drug therapy based on geneticprofiling (often referred to as pharmacogenetics).
Furthermore, efforts are underway to generate 3-D structures of a large number of target molecules in order todesign and develop drugs that are targeted against molecular structure and havethe least unwanted effects. The potential impact of genomics on drug discovery isProteomic and Genomic Analysis of Cardiovascular Disease.Edited by Jennifer E. van Eyk, Michael J. DunnCopyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 3-527-30596-334220 Genomics Perspective for Drug Discoveryevident from the fact that the current pharmacopoeia is based on products of lessthan 500 molecules [1], while the potential exists for the expansion of our pharmacological armamentarium to specifically target products of approximately 35,000genes that comprise the human genome [2]. Furthermore, genetic profiling – SNPand haplotype mapping – could also lead to more effective treatment of the responders and identification of those who are at risk of developing side effects.
Collectively, utilization of genome-based technology has the potential to introduce alarge number of “biotech” drugs into the market. In the year 2001, 6 “biotech”drugs were introduced, while the number is expected to double in 2002. Genomic-based drug discovery and treatment could also reduce the cost and the time ittakes to bring a product to the market. At the present time it is estimated that ittakes about US $500 million and 15 years to develop and market a drug [3]. In1998, the pharmaceutical industry spent approximately $20 billion in developingnew drugs [3].
Genomics, by providing for a more efficient target identificationand validation as well as more intelligent drug design and testing, could reducethe cost of developing new drugs. Altogether, genome-based drug discovery hasthe potential to revolutionize the practice of medicine in the coming years.20.2Human GenomeMiescher was the first to isolate DNA in 1869 [4]. However, the biological significance of this discovery was unrecognized until 1944, when Avery, McLeod andMcCarty [5] and Hershey and Chase later on in 1952 [6], showed DNA, ratherthan protein, was responsible for inheritance.
The works of Nobel Laureates Wilkins, Watson and Crick [7, 8] established the double-stranded structure of DNA andlaid the foundation of modern molecular biology and genetics. The birth of recombinant DNA technology occurred in 1970 with the discovery of a type II restriction enzyme in Hemophilus influenza [9], that along with identification ofDNA ligase three years earlier [10], made it possible to cut DNA at specific sitesand rejoin the DNA fragments. Subsequently, a DNA fragment was subclonedinto a self-replicating plasmid in vitro [11]. These advances, along with isolation ofDNA polymerases and reverse transcriptase [12], the development of techniques ofDNA sequencing [13], and the polymerase chain reaction [14] provided the milieunecessary for initiation of the Human Genome Project (HGP).
The HGP wasstarted in 1990 with the initial goal of developing genetic and physical maps ofthe human genome and ultimate goal of sequencing the entire genome. The project was successfully completed in 2001 several years ahead of schedule and thefirst draft of the human genome was published [2].The human genome is comprised of approximately 3.2 billion base pairs organized in approximately 35,000 genes and inter-genic regions [2]. Genes encodingproteins, the major interest of pharmacogenomics, comprise about 1% of the genome and the remainder is comprised of repeat sequences and segments with unknown function.
The most direct utility of genomics with regard to drug discovery20.3 Genomics and the Process of Drug Discoveryis to identify and characterize the encoded proteins from all genes in the humangenome (proteomics), which provide for the drug targets. Another powerful feature of the human genome is the presence of sequence variation among individuals, referred to as polymorphism. While > 99% of the genome sequence is identical between individuals, subtle variation in the sequence exists that are used tomap and identify the susceptibility genes for complex diseases and thus, identifynew drug targets.
The most common type of polymorphism is the single nucleotide polymorphism (SNP), which is estimated to occur 1 in every 300 bases in thehuman genome. Each gene is expected to contain several SNPs. Systematicscreening of a 5.5 kb fragment encompassing the gene encoding apolipoprotein Eshows 21 SNPs [15]. Similarly, at least 13 SNPs have been identified in a 27 kbfragment encompassing the angiotensin-1 converting enzyme 1 gene [16].
As ofDecember 13, 2001, the SNP database (dbSNP) for the human genome containsmore than 4.1 million SNPs (http://www.ncbi.nlm.nih.gov/SNP). The majority ofSNPs are located in the non-coding regions and are useful as genetic markers. Asmaller number of SNPs are located in the coding (cSNPs) and regulatory regionsof genes (rSNP) and thus, could affect structure or expression level of the encoded proteins. Therefore, SNPs are powerful tools not only for gene mappingand target identification, but also for delineating the genetic basis for the inter-individual variation in response to drug therapy (pharmacogenetics). The emphasisby the public and private consortiums is to develop SNP and haplotype maps ofthe human genome in order to perform a genome-wide search for the susceptibility genes for common diseases, such as atherosclerosis and hypertension, and toperform genetic profiling in order to individualize medical therapy.20.3Genomics and the Process of Drug DiscoveryThe current process of drug discovery could be classified into four stages of targetidentification, target validation, lead identification and lead validation.
The nextphase following drug discovery is to individualize therapy based on genetic information. We briefly discuss the potential impacts of genomics and the relatedsciences on each phase of drug discovery as well as individualization of drug therapy.20.3.1Genomics and Target IdentificationPerhaps, the most important contribution of genomics to drug discovery is towardunderstanding the molecular pathogenesis of human diseases. One direct consequence of such contribution is the identification of drug targets. Prior to the beginning of the modern era of molecular genetics, target identification was restricted by the ability to find and isolate new proteins.
Drug development also required a priori knowledge of involvement of the isolated proteins in the pathogen-34334420 Genomics Perspective for Drug Discoveryesis of disease of interest. Angiotensin-1 converting enzyme 1 (ACE-1) inhibitorsand b-blockers were developed when experimental data suggested their involvement in the pathogenesis of heart failure and hypertension. The approach of isolating and identifying a protein as the initial step for drug discovery, while tedious, has led to identification of the vast majority of the current cardiovasculardrugs, such as ACE-1 inhibitors, angiotensin II receptor 1 blockers, b-blockers,thrombolytics, IIb/IIIa inhibitors, and endothelin-1 receptor blockers.
The limitednumber of known proteins, however, hinders the utility of this approach in drugdiscovery. As a result, our current pharmacopoeia is aimed at approximately 500molecules, the majority of which are targeted to a few receptors and enzymes [1].As such, over 50% of our current drugs directly affect G protein coupled receptors[1]. The genomic approach, which initially was referred to as “the reverse genetics”, does not require a priori isolation of the encoded proteins or a priori knowledge of the candidate gene in the pathogenesis of the disease. Instead, potentialdrug targets are identified through the use of genomic tools. Accordingly, thenumber of proteins and their isoforms encoded from the approximately 35,000genes in the human genome determines the number of potential drug targets.
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