You are here Biopharmaceutical/ Genomic Glossaries homepage/Search > Pharmaceutical Applications

21st century drug discovery & development overview & taxonomy
Evolving terminology for emerging technologies
Comments? Revisions? Questions?  Mary Chitty mchitty@healthtech.com
Last revised March 28, 2008
View a Printer-Friendly Version of this Web Page!

Finding guide to terms in these glossaries  Pharmaceutical applications map,   Site Map

analyte specific reagents:  A new class of regulated product: analyte specific reagents. These products are usually a singular reagent, such as an antibody, which can be used toward developing a test by third parties, such as another company or a hospital. The manufacturer of this product is not planning to sell it as part of a kit, but only as an independent reagent. Therefore, it is of low risk to the user, it can be exempt from 501(k) [device] requirements, and by definition must be used "for identification and quantification of an individual chemical substance or ligand in biological substances." Joseph Hackett, FDA  in CHI Summit Pharmacogenomics Report]  Drug approvals & clinical trials glossary

Beyond Genome: By combining RNAi, Systems Biology, Proteomics, and Alternative Splicing Beyond Genome allows a rare opportunity to connect with colleagues within these respective fields. Beyond Genome, June 20-22, 2008, San Francisco CA

biochemical pathways: The identification and validation of drug targets depends critically on knowledge of the biochemical pathways in which potential target molecules operate within cells. For this reason, the study of biochemical pathways is the focus of numerous researchers and is central to the strategy of many biopharmaceutical and genomic companies.   Metabolic engineering glossary 

blockbuster drugs: Defined as drugs with $1 billion or more in sales.  Mega- blockbusters are drugs with sales of $1 billion plus in their first year.  IMS Health, Market Insight, Mar. 19, 2002 http://www.ims-global.com/insight/news_story/0203/news_story_020317.htm Business of biopharmaceuticals glossary

burn rate: The rate at which a company (not yet making a profit) is going through its available money (which may come from angel investors, venture capital and other sources).. Generally expressed in cash spent per month.  Financial glossary

cancer genomics:  Technology is enabling ever increasingly rapid DNA analysis and, with that, the ability to establish personalized genome analysis. This has opened up the possibility of determining an individual's susceptibility to cancer at birth, and at selected periods during his or her life. In addition, the technology is enabling the identification of genetic components in cancer at the cellular and molecular levels - factors that will help identify new therapeutic targets and facilitate more effective selection of the drugs currently available on a patient- by- patient basis. CHI Cancer Genomics: Commercial Developments and Identification of New Molecular Targets for Therapy  report  Cancer genomics & proteomics glossary  

cancer proteomics: The use of DNA microarrays to study cancer is as established as the technology itself [5, 6]. Transcriptome data is not only used to classify different types of cancer, but to shed light on known and unknown cancer genes: proto- oncogenes, oncogenes, and tumor suppressor genes. Proteome data, on the other hand, is not as pervasive, largely due to technological limitations. However, with the steady advancements in the tools mentioned above, “cancer proteomics” is becoming a reality. James Kuo "Proteomics and its applications to cancer research" Molecular Biology & Biochemistry, Yale Univ. 2000  http://bioinfo.mbb.yale.edu/mbb452a/2000/projects/James--Kuo.html   Cancer genomics & proteomics glossary 

drug repositioning: Involves determining novel uses for existing drugs and rescuing failed compounds. Major benefits of this approach include shorter development cycles, faster drug approval, and the ability to capitalize on the repertoire of drug candidates. Different approaches will be presented for identifying additional indications for compounds, screening against new targets, evaluating patent life, and identifying medical need. Lessons learned will include how to harness creativity to invent new niche markets or diseases. Drug repositioning: Finding New Routes to Success, Oct. 16-17, 2006, Philadelphia PA  Drug Discovery & Development glossary 

druggable: Able to be modulated by a small molecule to produce a desired phenotypic change in cell targets.   

Variant spelling is drugable, however Google has about 283 hits for druggable (Nov. 16, 2001; 545 May 2002) with about 138 for drugable (Nov. 16, 2001; 248 May 10, 2002). Drug Discovery & Development glossary 

functional genomics:  Aims to discover the biological function of particular genes and to uncover how sets of genes and their products work together in health and disease. In its broadest definition, functional genomics encompasses many traditional molecular genetic and other biological approaches. Functional Genomics glossary 

genetic testing: Allen Roses, worldwide director of genetics for Glaxo Wellcome [now Glaxo SmithKline] notes  "Until now, government sponsored committees convened to address ‘genetic testing’ have generally limited their definition and their reports to concerns regarding diseases caused by single gene mutations … Another class of  'genetic tests’ is related to pharmacogenetics, including ... variants or other inherited polymorphic traits that are not diagnostic of disease … Clear language and differentiation of respective ethical, legal and societal issues are required to prevent inaccurate vernacular usage creating a confused public perception. Allen Roses, Pharmacogenetics and the practice of medicine” Nature 405: 857- 865, 15 June 2000   Genetic & genomic testing glossary  

genomics:  Generation of information about living things by systematic approaches that can be performed on an industrial scale. Roger Brent "Genomic biology" Cell 100: 169-183 Jan 2, 2000 

The systematic study of the complete DNA sequences (GENOME) of organisms. [MeSH, 2001] 

Coined by Thomas H. Roderick [of the Jackson Laboratory, Maine, US] in 1986 in Bethesda, MD during a discussion of a name for a planned new journal (Genomics) that was to include sequencing data, discovery of new genes, gene mapping, and new genetic technologies. According to Roderick, the term genomics "also had the comparative aspect of genomes of various species, their evolution, and how they related to each other. Although we didn't come up with the term ‘functional genomics’ we thought of the genome as a functioning whole beyond just single genes of sequences spread around a chromosome." B Kuska "Beer, Bethesda, and Biology" JNCI 90(2): 93, Jan 21,1998  Genomics glossary 

Human Genome Project HGP: Horace Freeland Judson writes in "Talking about the genome" (Nature 409:769, 15 Feb. 2001) "The language we use about genetics and the genome project at times limits and distorts our own understanding, and the public understanding. Look at the phrase - or marketing slogan - 'the human-genome project'. In reality, of course we have not just one human genome but billions. ... Then, too, the entire phrase - the human- genome project: singular, definite, with a fixed end- point, completed by 2000, packaged so it could be sold to legislative bodies, to the people, to venture capitalists. But we knew from the start the genome project would never be complete. 

A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human genome. MeSH, 1990  Genomics glossary

low hanging fruit: The easiest drugs to identify and gain approval for.  The big question these days is whether there is any "low hanging fruit" left. Related terms druggable, pharmaceutically tractable, tractable targets  Drug Discovery & Development glossary 

Mendelian genetics: Classical genetics, focuses on monogenic genes with high penetrance, the tip of the iceberg of genetics.  Basic genetics & genomics briefly explains of how genetics and genomics differ. Genomics is both a narrower and broader term than genetics. Genomics glossary

patent pooling: A patent pool is an agreement between two or more patent owners to license one or more of their patents to one another or third parties. A patent pool allows interested parties to gather all the necessary tools to practice a certain technology in one place, e.g, "one- stop shopping," rather than obtaining licenses from each patent owner individually. US Patent and Trademark Office "USPTO issues white paper on patent pooling" Jan. 19, 2001 http://www.uspto.gov/web/offices/com/speeches/01-06.htm  Intellectual property & legal glossary

pathways: The routes or processes by which genes and their products function in cells, tissues, and organisms. Pathways involving a particular gene or its product may be determined by two major types of methods. One involves identifying other proteins that specifically interact with the product of the gene of interest. The other involves carrying out specific genetic studies with model organisms. Networks are composed of pathways. We are just beginning to untangle some basic understanding of pathways, and understanding of their interrelationships lies ahead.  Narrower terms: biochemical pathways, metabolic pathways Metabolic engineering glossary 

phage display: Selection systems of biologically- active molecules are essential to pipeline of novel protein therapeutics which can be directed against targets that are intractable to small molecules. Phage display and related techniques such as mRNA, bacteria, yeast, antibody, ribosome display offer the ability to generate and select ligands against biologic mechanisms, and engineer drug- like properties into candidates that show high affinity and specificity. Novel scaffolds will be considered for many reasons, including the ease of synthesis and the ability to address new drug targets. This meeting will focus on the technologies used to optimize protein and peptide entities against targets, and the refinement of these methods for clinical application against cancer, AIDS, autoimmune, infection, and other diseases.  Phage Display Therapeutics: Engineering Selection Systems, April 24 -25, 2006, Boston MA    Genetic Manipulation & Disruption glossary

pharmacogenomics: The analysis of genomics- based variation in drug response. This practice can potentially help clinicians administer more tailored treatment. CHA  Toxicogenomics: The Promise of Safer, Smarter Drug Development report

From pharmacology +  genomics. Pharmacogenomics glossary  Related terms: Biomarkers glossary

pharming: Use of  transgenic animals to produce drugs in their milk, urine or eggs.  Transgenic plants can also be used. (Tobacco is said to be particularly amenable to this application).  Drug Discovery & Development glossary 

post-genomic: The genome era is generally regarded to have started on 28 July 1995, with the publication of the genome of the bacterium Haemophilus influenzae. ["A point of entry into genomics" Nature Genetics 23:273 Nov. 1999] Still, in most contexts talk about being  "post- genomic" seems a little premature. "Post- Mendelian" seems more accurate as we move from an era in which genetics has been rooted in monogenic diseases with high penetrance to a greater awareness (but limited understanding) of polygenic diseases (and traits) often with relatively low penetrance. Post- genomic can also refer to the increasing emphasis on functional genomics  Beyond Genome: Top 10 Opportunities in the Post Genome Era, June 19-21, 2006, San Francisco, CA  Genomics glossary  

proteomics: The most useful definition of proteomics is likely to be the broadest: proteomics represents the effort to establish the identities, quantities, structures and biochemical and cellular functions of all proteins in an organism, organ, or organelle, and how these properties vary in space, time and physiological state. .. A much broader field than would be apparent from early efforts, which have focused on cataloging levels of protein expression.  Ideally it should encompass efforts to obtain complete functional descriptions for the gene products in a cell or organism. Defining the Mandate of Proteomics in the Post- Genomics Era, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html  Proteomics glossary

RNAi RNA interference:  The Nobel Prize in Physiology & Medicine for 2006 was awarded to two excellent researchers for their discovery of RNA interference. This illustrates just how far gene silencing by double-stranded RNA has come in a relatively short amount of time. RNA-based silencing has created an enormously powerful tool for validation of drug targets. Even more recently RNAi therapeutic development has raced ahead at great speed with much excitement. In vivo delivery, tissue specificity and toxicity are among the challenges to developing successful therapeutic agents. Dealing with off-target effects in siRNA screening is still a challenge and recent research points to similar findings with shRNA. Approaches such as use of multiple siRNA’s per gene and other controls will be discussed as well as a look at knockdown validation studies. Developing lentivirus-based systems will be explored with case studies using primary cell lines and some discussion of the microRNA space will be included. Beyond Genome: RNAi, June 19-20, 2007, San Francisco CA  Genetic manipulation & disruption glossary

small molecules: Preferred for drugs as they are orally available (unlike proteins which must be administered by injection or topically). Size of small molecules is generally under 1000 Daltons, but many estimates seem to range from between 300 to 700 Daltons. Drug Discovery & Development glossary  

strategic alliances: May refer to a joint venture or an alliance network. Strategic implies that one (or each) companies have something unique to bring to the agreement. (Not all alliances are as strategic as their participants initially hoped for.) May well involve more than two entities.  Alliance Management Congress May 8-9, 2006 • Philadelphia PA  Alliances glossary

structural genomics: The discipline of determining protein structures. It adds critical information in at least two points in the drug discovery pathway: (1) target identification, or selecting a pathway in which a drug might function, and (2) medicinal chemistry, or the actual design of compounds to modulate this pathway.  As traditionally defined, the term structural genomics referred to the use of sequencing and mapping technologies, with bioinformatic support, to develop complete genome maps (genetic, physical, and transcript maps) and to elucidate genomic sequences for different organisms, particularly humans. Now, however, the term is increasingly used to refer to high- throughput methods for determining protein structures)  Structural Genomics glossary

target validation: Demonstrating that a molecular target is critically involved in a disease process, and that modulation of the target is likely to have a therapeutic effect. CHA, Cambridge Healthtech Advisors Model Animal Systems: Emerging Applications and Commercial Opportunities in Drug Discovery and Development report 

Target validation, Beyond genome June 19-21, 2006, San Francisco CA  The target is truly validated only after it is proven effective in human trials.  Targets glossary

toxicogenomics: In its strictest definition, refers to the use of DNA microarray technology to identify patterns of gene expression that can be used to predict human toxicity of new drug candidates or other potential toxicants. The concept is based on the hypothesis, proven in only a preliminary sense, that a finite and limited set of such patterns, or signatures, exists and that these signatures are, in fact, highly predictive CHI report Toxicogenomics: The Promise of Safer, Smarter Drug Development 

translatome: The cellular population of proteins expressed in the organism at a given time, explicitly weighted by their abundance. ... Our definition of the translatome is partially motivated by the ambiguities in term proteome, which has two competing definitions. First, broadly favoured by computational biologists, is a list of all the proteins encoded in the genome (Gaasterland 1999, Doolittle 2000). In this context, it is equivalent to what some refer to as the ORFeome, i.e. the set of genes excluding non- coding regions. Experimentalists, especially those involved in large- scale experiments such as expression analysis and 2D electrophoresis, favor a second definitions. Here it is used to describe the actual cellular contents of proteins, taking into account the different levels of protein concentrations (Yates 2000). We prefer the former definition for proteome, and use the term translatome for the later.  Dov Greenbaum "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf    -Omes & -Omics glossary 

Bibliography

Alpha glossary index