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Drug discovery & development overview
Evolving terminology for emerging technologies
Comments? Revisions? Questions? 
Mary Chitty MSLS mchitty@healthtech.com
Last revised March 22, 2018
 

Finding guide to terms in these glossaries  Drug discovery & Development term index  

analyte specific reagents:  Antibodies, both polyclonal and monoclonal, specific receptor proteins, ligands, nucleic acid sequences, and similar reagents which, through specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological specimens.  Title 21  Food and Drugs  Chapter I FDA Dept HHS Subchapter H Medical Devices Part 809 IN VITRO DIAGNOSTIC PRODUCTS FOR HUMAN USE Subpart C--Requirements for Manufacturers and Producers http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?FR=809.30   Regulatory Affairs

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 

blockbuster drugs: Mega blockbusters (or drugs that have sold more than $10 billion in sales per year) and super blockbusters (or drugs that have sold more than $2 billion each annually). Though pharma growth slides blockbusters reach new record, WTN News 2005 http://wistechnology.com/articles/1885/  Blockbuster drugs have sales of $1 billion plus  Business of biopharmaceuticals

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

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.  Cancer  

drug-like, drug-likeness: There are currently about 10000 drug-like compounds. These are sparsely, rather than uniformly, distributed through chemistry space. True diversity does not exist in experimental combinatorial chemistry screening libraries. Absorption, distribution, metabolism, and excretion (ADME) and chemical reactivity-related toxicity is low, while biological receptor activity is higher dimensional in chemistry space, and this is partly explainable by evolutionary pressures on ADME to deal with endobiotics and exobiotics. ADME is hard to predict for large data sets because current ADME experimental screens are multi-mechanisms, and predictions get worse as more data accumulates. Drug-like properties and the causes of poor solubility and poor permeability.Lipinski CA. J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49  Drug Discovery & Development

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 Discovery & Development 

druggable: Able to be modulated by a small molecule to produce a desired phenotypic change in cell targets.   Variant spelling is drugable, however on Feb 22 2011 Google has about 67,900 hits for druggable Feb 22 2011 and about 20,500 for drugable . Drug Discovery & Development 

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

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   Molecular diagnostics  

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

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

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

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 paent pooling" Jan. 19, 2001 http://www.uspto.gov/web/offices/com/speeches/01-06.htm  Intellectual property & legal

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

pharmacogenomics: Despite their slightly different definitions, as with other "-genetics" and "-genomics" terms, pharmacogenomics (PGt) and pharmacogenomics (PGx) are often used interchangeably.  This is not surprising since both terms refer to the study or use of genetic variation in drug responses. PGx is also often used as the more all-encompassing, or default, term when referring to the general study or use of genetic variation in drug response. ... There really isn't clear consensus (yet) on the best definitions for each term. Insight Pharma Reports, Pharmacogenomics: Delivering on the promise, 2009 

Comprises the study of variations in targets or target pathways, variation in metabolizing enzymes (pharmacogenetics) or, in the case of infectious organisms, genetic variations in the pathogen. CHI Drug Discovery Map http://www.healthtech.com/drugdiscoverymap.asp

For the purposes of this guidance, the term pharmacogenomics is defined as the use of a pharmacogenomic or pharmacogenetic test (see glossary for definitions) in conjunction with drug therapy. Pharmacogenomics does not include the use of genetic or genomic techniques for the purposes of biological product characterization or quality control (e.g. cell bank characterization, bioassays). The FDA plans to provide guidance on those uses at a future time. Pharmacogenomics also does not refer to data resulting from proteomic or metabolomic techniques.  This document is not meant to provide guidance on pharmacoproteomics or multiplexed protein analyte based technologies. Guidance for Industry, Pharmacogenomic Data Submissions CDER, CBER, CDRH, FDA,  March 2005  Non-binding recommendations.  http://www.fda.gov/cber/gdlns/pharmdtasub.pdf 

From pharmacology +  genomics. Pharmacogenomics  Related terms: Biomarkers

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    Genomics  

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

RNAi RNA interference:  RNAi gene silencing phenomenon whereby specific dsRNAs ( RNA, DOUBLE- STRANDED) trigger the degradation of homologous mRNA ( RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA- INDUCED SILENCING COMPLEX (RISC). DNA METHYLATION may also be triggered during this process. MeSH 2003    Genomic Technologies

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  

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.  Alliances

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)  Protein informatics

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.  The target is truly validated only after it is proven effective in human trials.  Drug & diseases Targets

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 

Bibliography