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Drug targets & disease targets glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty 
mchitty@healthtech.com
Last revised September 10, 2014

 



The true test of validation comes only when a selective inhibitor for the chosen target is advanced to the clinic and shown to be efficacious in the appropriate human disease. However, advancing the wrong target to this stage is a costly mistake. Much of the impact of genomics on drug development thus far has been focused on the identification and validation of biological targets. While much of this research on targets is based only on comparisons of the biology of health and disease, sooner or later it becomes critical to integrate the activity of chemical compounds with the body.

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allosteric modulators: Allosteric modulation of GPCRs is rapidly emerging as a major area of interest for pharmaceutical discovery because allosteric modulators have the potential to show dramatically improved safety, tolerance, and side-effect profiles compared to traditional orthosteric agonists and antagonists. Allosteric Modulators October 2-3, 2012 • Boston, MA Program | Register | Download Brochure Allosteric Modulators

binding, competitive:
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements. MeSH 1973

binding site: A specific region (or atom) in a molecular entity that is capable of entering into a stabilizing interaction with another molecular entity. IUPAC Bioinorganic

The reactive parts of a macromolecule that directly participate in its specific combination with another molecule. MeSH, 1968 Related terms: ligand; receptor mapping. Narrower term: binding sites, antibody 

binding sites, antibody: Local surface sites on antibodies which react with antigen determinant sites on antigens. They are formed from parts of the variable regions of the Fab fragment of the immunoglobulin. MeSH, 1973

biological target http://en.wikipedia.org/wiki/Biological_target  See also  Drug discovery informatics drug design 

cancer cell metabolism: The fact that cancer cells have an altered glucose metabolism has sparked new interest in the pharmaceutical industry. Reversing the increased glucose consumption in cancer cells is an important step and has great potential for therapeutic drug developments. Targeting Cancer Cell Metabolism October 1-2, 2012 • Boston, MA Program | Register | Download Brochure  Targeting Cancer Cell Metabolism  

cancer stem cells targeting: Targeting Cancer Stem CellsTargeting Cancer Stem Cells February 13-14, 2014 • San Francisco, CA Program | Register | Download Brochure

channel blocker,  Compound that reduces or eliminates the conductance of an ion channel by impeding the movement of ions through that channel  IUPAC Biomolecular Screening   See also ion channels.

Chemical Biology for Target ValidationChemical Biology for Target Validation  May 22-23, 2014 • Boston, MA

Program | Register | Download Brochure

chemical ligand studies: Use a more general set of compounds [than chemical genomics] (often from combinatorial libraries) to find new targets. Once the new targets are found, more specific assays are done. In other words, with the chemical ligands approach, one does blind screening of chemical libraries using cellular assays. When one gets an interesting biological effect, one uses the compound to find the target it modulates. [The precise definition of the following terms varies widely between drug discovery companies. The meanings given here are aligned with the use of the terms within the lead discovery function at GlaxoWellcome.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery" Drug Discovery Today 5(7): July 2000 

chemogenomics:  British Journal of Pharmacology, 2007 http://www.nature.com/bjp/journal/v152/n1/full/0707308a.html 

Chimeric Antigen Receptors (CAR): Recombinant receptors that provide both antigen-binding and T-cell-activating functions. A multitude of CARs has been reported over the past decade, targeting an array of cell surface tumor antigens. … CARs are a new class of drugs with great potential for cancer immunotherapy. Upon their expression in T lymphocytes, CARs direct potent, targeted immune responses that have recently shown encouraging clinical outcomes in a subset of patients with B-cell malignancies. The basic principles of chimeric antigen receptor design. Sadelain M, Brentiens R, Riviere I, Cancer Discov. 2013 Apr; 3 (4): 388-398. doi: 10.1158/2159-8290.CD-12-0548. Epub 2013 Apr 2. http://www.ncbi.nlm.nih.gov/pubmed/23550147

compound profiling: Biology has considerable experience with gene and protein- centered informatics, but chemistry is at an earlier stage of developing databases that are truly compound- centric. The historical paradigm of identifying and optimizing hits for potency, and then looking to evaluate and optimize for ADME and toxicity properties is quickly shifting to a more parallel approach that considers ADME/Tox properties at an earlier stage. This concept is epitomized by methods for differentiating between drug- like and non- drug- like compounds, the use of which is increasing significantly. Moving compound profiling earlier means that many more compounds must be assessed, which is both the value and the challenge of this shift.  http://www.healthtech.com/Conferences/2007/cpf/index.asp 

compound validation: Assays & screening

cytokine-based therapeutics: Emerging cytokine-based therapies, and inhibitors of cytokines and their receptors, represent attractive markets that have become highly competitive. More than 120 companies are developing over 270 new therapies that either are cytokines, mimic cytokines, or inhibit cytokines and/or cytokine receptors. Cytokine-Based Therapies and Inhibitors:R&D Pipelines, Markets, and Strategic Issues September 2011 Table of Contents | Tables and Figures |Executive Summary


Related term: Protein categories: cytokines 

cytoplasmic and nuclear receptors: Proteins in the cytoplasm or nucleus that specifically bind signaling molecules and trigger changes which influence the behavior of cells. The major groups are the steroid hormone receptors (RECEPTORS, STEROID), which usually are found in the cytoplasm, and the thyroid hormone receptors (RECEPTORS, THYROID HORMONE), which usually are found in the nucleus. Receptors, unlike enzymes, generally do not catalyze chemical changes in their ligands. MeSH, 1994

deorphanize: Identification of new ligands for receptors.
Discovery on Target

Discovery on Target October 8-10, 2014 • Boston, MA Program | Register | Download Brochure

Discovery on Target
 

disease targets:
The critical strategy for a pharmaceutical company going forward is one that uses pharmacogenomics and biomedical informatics to better define disease targets. ...  Pharmacogenomics is key to gaining a better definition of disease, a better stratification of patients and improved disease staging. Until these are clear, and until some form of biomedical informatics is put into place, therapeutic design is going to be flawed by poorly defined targets. Broader term: target Related term: drug target  

drug leads: small molecule ligands  DS Wishart Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking. Methods Mol Biol. 2008;443:333-51.

drug receptors: Proteins that bind specific drugs with high affinity and trigger intracellular changes influencing the behavior of cells. Drug receptors are generally thought to be receptors for some endogenous substance not otherwise specified.  MeSH, 1968  Broader term: receptors

drug target, drug targets:  An unspoken industry rule alleges that at least 50% of published studies from academic laboratories cannot be repeated in an industrial setting, wrote venture capitalist Bruce Booth in a recent blog post. A first-of-a-kind analysis of Bayer's internal efforts to validate 'new drug target' claims now not only supports this view but suggests that 50% may be an underestimate; the company's in-house experimental data do not match literature claims in 65% of target-validation projects, leading to project discontinuation. Nature Reviews Drug Discovery 10, 643-644 (September 2011) | doi:10.1038/nrd3545 Reliability of 'new drug target' claims called into question Asher Mullard http://www.nature.com/nrd/journal/v10/n9/full/nrd3545.html

A prerequisite for counting the number of targets is defining what a target is. Indeed, this is the crucial, most difficult and also most arbitrary part of the present approach. For the purpose of this paper, we consider a target to be a molecular structure (chemically definable by at least a molecular mass) that will undergo a specific interaction with chemicals that we call drugs because they are administered to treat or diagnose a disease. The interaction has a connection with the clinical effect(s).  This definition implies several constraints. First, the medicinal goal excludes pharmacological and biochemical tools from the present approach. Second, a major constraint is a lack of technique. Life, including disease, is dynamic, but as we do not yet directly observe the interactions of drugs and targets, and only partly notice the subsequent biochemical 'ripples' they produce; we are generally limited to 'still life' (for example, X-ray crystal structures) and to treating targets as static objects. In the case of G-protein-coupled receptors (GPCRs), the pharmaceutically most useful class of receptors, a re-organization of the protein after drug binding was derived from biochemical data4, but such approaches are still in their infancy. Nature Reviews Drug Discovery 5, 821-834 (October 2006) | doi:10.1038/nrd2132  OPINIONDrugs, their targets and the nature and number of drug targets Peter Imming1, Christian Sinning1 & Achim Meyer1 http://www.nature.com/nrd/journal/v5/n10/full/nrd2132.html

Good drugs are potent and specific; that is, they must have strong effects on a specific biological pathway and minimal effects on all other pathways. Confirmation that a compound inhibits the intended target (drug target validation) and the identification of undesirable secondary effects are among the main challenges in developing new drugs. Matthew J. Morton et. al, Drug target validation and identification of secondary drug target effects using DNA Microarrays,  November 1998 4 (11): 1293 - 1301, Nov. 1998  Related terms:  molecular drug targets, target families. Narrower terms: gene target, protein target    targets  

How many drug targets are there? John P Overington, et. al, Nature Reviews Drug Discovery, 2006 http://www.nature.com/nrd/journal/v5/n12/pdf/nrd2199.pdf 

drug targeting: Drug delivery

DrugBank: a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. DrugBank is supported by David Wishart, Departments of Computing Science & Biological SciencesUniversity of Alberta.  DrugBank is also supported by The Metabolomics Innovation Centre, a Genome Canada-funded core facility serving the scientific community and industry with world-class expertise and cutting-edge technologies in metabolomics.  http://www.drugbank.ca/

druggable targets: a protein, peptide, or nucleic acid with activity that can be modulated by a drug, which can consist of a small molecular weight chemical compound (SMOL) or a biologic [BIOL) such as an antibody or recombinant protein (Table 1). Isabella Gashaw, Peter Ellinghaus, Anette Sommer, Khrusru Asadullah "What makes a good drug target" Drug Discovery Today 2011 Dec;16(23-24):1037-43. Epub 2011 Sep 16. http://www.ncbi.nlm.nih.gov/pubmed/21945861.1

"We have historically fewer innovative targets per year", said Christopher Lipinski, formerly of Pfizer, showing that only 24 innovative drugs with new targets have been launched between 1994 and 2001 "Many more druggable targets may have emerged in these eight years, but there are not enough druglike molecules to match them", Lipinski said. Horizon Symposia 4 Charting Chemical Space, 2004 . http://www.nature.com/horizon/chemicalspace/highlights/s3_nonspec2.html

efficacy targets: Molecular targets through which the drug mediates its approved therapeutic activities. John P Overington et. al How many drug targets are there? Nature Reviews Drug Discovery, 5 (12): 993-996 Dec 2006 http://www.nature.com/nrd/journal/v5/n12/pdf/nrd2199.pdf 

emerging targets: The report assesses the issues in target-based drug discovery and development as well as several specific issues that are common to these and other complex diseases with high unmet medical need. … Evaluation of leading emerging targets in terms of signaling pathways and therapeutic strategies. Insight Pharma Reports Emerging Targets in Disease with High Unmet Needs, 2006

Epigenetic Inhibitor Discovery April 23-24, 2014 • San Diego, CA Program | Register | Download Brochure

Epigenetics: Emerging Targets, Available Technologies, Expert Interviews, and an Epigenetic Community Perspective
October 2013

gene target: Having identified a potential gene target (and, by inference, its protein product), one may wish to: (a) sequence the gene in a large number of affected and normal individuals to identify functional and diagnostic polymorphisms associated with the disease; or (b) rapidly screen the protein product for interactions with entities within the chemical portfolio of the company. Clearly, these needs are addressed by very different approaches and technological platforms, all of which may be defined as high throughput genomic strategies. 

gene targeting: The integration of exogenous DNA into the genome of an organism at sites where its expression can be suitably controlled. This integration occurs as a result of homologous recombination. MeSH, 1995  

G-protein-coupled receptors GPCRs:  The GPCR program will continue its tradition of combining theory with screening and optimization strategies illustrated by case studies of drug candidates in development. Topics to be covered at this year’s meeting will include exploiting ligand-biased signaling; receptor desensitization, internalization and recycling in the context of developing drug candidates; new tools and technologies (functional screens, label-free assays); drug discovery Implications of recent GPCR crystal structures ; structure-based design strategies and therapeutic antibodies.  

Current advances in functional screening methodologies, medicinal chemistry, and structure-based drug design have generated large increases in the number and diversity of GPCR drug targets. Furthermore, basic research advances have opened the way for still further exploitation of this target class. Insight Pharma Reports, GPCRS: Dawn of a new era? 2008

The largest family of cell surface receptors  involved in SIGNAL TRANSDUCTION. They share a common structure and signal through HETEROTRIMERIC F- PROTEINS  MeSH 2004 "receptors, g-protein coupled". Narrower terms: orphan G- protein coupled receptors, GPCRomics

histone deacetylases: Histone deacetylases (HDACs) have proven to be a promising target for drug intervention and there are a number of HDAC inhibitors (HDACi) being tested in the pre-clinical and clinical stages. HDACi were primarily developed as anti-tumor agents for cancer, but many are now being explored for treating CNS, immunologic, metabolic, inflammatory and cardiovascular disorders.


histone methyltransferases: Histone methyltransferases (HMTs) and demethylases (HDMs) have rapidly emerged within the suite of epigenetic modifiers as new and promising classes of therapeutic targets. Recent genetic discoveries of HMT and HDM anomalies in various cancer types provide unique validation for selective and tumor-specific targeting of these enzymes. Clinical intervention is becoming increasingly feasible, but deciphering their role in complex disease, developing robust screening and hit-finding approaches for inhibitors, and assessing patient-specific efficacy and safety of novel therapies remain challenging. 

ion channels: Gated, ion-selective glycoproteins that traverse membranes. The stimulus for channel gating can be a membrane potential, drug, transmitter, cytoplasmic messenger, or a mechanical deformation. Ion channels which are integral parts of ionotropic neurotransmitter receptors are not included. MeSH 1979 
Ion channels as therapeutic targets, Discovery on Target Nov 2010 Boston MA
 order CD 

Enable ions to flow rapidly through membranes in a thermodynamically downhill direction after an electrical or chemical impulse. IUPAC Bioinorganic
Ion Channel Modulator Pipelines  Insight Pharma Reports, September 2009 Table of Contents | Tables and Figures | Executive Summary   See also channel blockers

kinase inhibitors: Kinase Inhibitor Chemistry  April 24-25, 2014 • San Diego, CA Program | Register | Download Brochure

kinase therapeutics: The field of kinase modulation is one of the most active in the biopharmaceutical industry. About 20 kinase inhibitors are approved for marketing in the United States and at least another 250 are in clinical evaluation. Kinases make up a veritable treasure trove of targets for a variety of indications. Kinase-Targeted Therapeutics August 2011Table of Contents | Tables and Figures |Executive Summary

Related terms:  kinase inhibitors, protein kinases 

ligand: In inorganic chemistry the ligands are the atoms or groups of atoms bound to the central atom (see also coordination). The root of the word is sometimes converted into the verb to ligate, meaning to coordinate as a ligand, and the derived participles, ligating and ligated…In biochemistry the term ligand has been used more widely: if it is possible or convenient to regard part of a polyatomic molecular entity as central, then the atoms or groups or molecules bound to that part may be called ligands. IUPAC Bioinorganic

Pharmacologists traditionally divide ligands into agonists, which stimulate receptors, and antagonists, which bind to receptors and block endogenous mediators. According to the conventional view, the agonist fits into the receptor, like a key fits a car's ignition, switching on the internal machinery. Antagonists fit the ignition, but block endogenous transmitters. But recent studies suggest that many receptors spontaneously activate internal machinery. In these cases, the receptor is more akin to an accelerator. Mark Greener, Driving Changes in Ligand Theory, The Scientist 18(15): 32, Aug. 2, 2004 http://www.the-scientist.com/yr2004/aug/research4_040802.html 

A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed) MeSH 1974 

Molecules (e.g., drugs) that bind to active sites on proteins. Particularly used of small molecules that bind to larger molecules. Narrower term: protein ligand; Related terms: antigen, binding site,  enzyme- substrate, hormone- receptor reaction, lock and key  

ligand design: The design of ligands using structural information about the target to which they should bind, often by attempting to maximize the energy of the interaction. IUPAC Computational

ligand gated ion channels: A subclass of ion channels that open or close in response to the binding of specific LIGANDS. MeSH 2011

membrane proteins: Protein categories  Important as drug targets

mitochondrial dysfunction: Targeting Mitochondrial Dysfunction & ToxicityTargeting Mitochondrial Dysfunction & Toxicity  March 19-20, 2014 • Boston, MA Program | Register | Download Brochure

molecular drug targets: Current Drug Targets aims to cover the latest and most outstanding developments on the medicinal chemistry and pharmacology of molecular drug targets e.g. disease specific proteins, receptors, enzymes, genes. Current Drug Targets scope note, Bentham Science http://www.bentham.org/cdt/index.htm  See also molecular targets  

Molecular Pharmacopeia
http://www.nature.com/focus/molecularpharmacopoeia/index.html 2006  For the past decade, the number of molecular targets for approved drugs has been debated. However, if we are to develop predictive methods to identify potential new drug targets, it is important that we establish with confidence the number, characteristics and biological diversity of targets of approved drugs.

molecular profiling: A dynamic new discipline, capable of generating a global view of mRNA, protein patterns, and DNA alterations in various cell types and disease processes.  MP integrates the expanding genetic databases from the Human Genome Project with newly developed expression analysis technologies and holds great promise to help us: Understand the molecular anatomy of normal cells and cells in various stages of disease.  Develop new diagnostic and therapeutic targets for clinical intervention. Explain the relationship between genotype and phenotype in humans, which is still largely unknown. NCI, NIH CGAP "Molecular Profiling"  http://cgap-mf.nih.gov/index.html  See also Expression gene & protein

molecular targeted therapy: Treatments with drugs which interact with or block synthesis of specific cellular components characteristic of the individual's disease in order to stop or interrupt the specific biochemical dysfunction involved in progression of the disease. MeSH 2011

molecular targeting: The idea behind molecular targeting is to design drugs that specifically attack the molecular pathways that cause disease, without disrupting the normal functions in our cells and tissues. Drugs developed using this approach can be less toxic and more effective than current medicines. Molecular Targeting, PhRMA, innovation.org http://www.innovation.org/index.cfm/FutureofInnovation/NextWaveofInnovation/Molecular_Targeting

molecular targets:  Collections of genes organized by pathways and by ontology (functional classification) permitting aggregate evaluation of anomalies (overexpression, underexpression, mutation). Molecular Targets, Cancer Molecular Analysis Project, National Cancer Institute http://cmap.nci.nih.gov/Targets   Can include antibodies, enzymes, receptors.  See also molecular drug targets   

multi-targeted therapies: Suites of drugs have been developed that can be used in combination to treat complex diseases that have multiple causes involving multiple targets. In addition, it has been found that many successful small-molecule drugs are promiscuous, i.e., they are single drugs that address multiple targets. Multitargeted Therapies June 2011 Table of Contents | Tables and Figures  Related terms: promiscuous drugs, promiscuous inhibitors

 

NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA- binding subunits: NF-kappa B1 and relA. MeSH, 1991  Related terms: cytokines  Wikipedia http://en.wikipedia.org/wiki/NF-%CE%BAB

nodal signaling ligands: Members of the transforming growth factor superfamily that play a role in pattern formation and differentiation during the pregastrulation and GASTRULATION stages of chordate development. Several nodal signaling ligands are specifically involved in the genesis of left-right asymmetry during development. The protein group is named after a critical region of the vertebrate embryo PRIMITIVE STREAK referred to as HENSEN'S NODE. MeSH 2009 

Novel Drug Targets and Screening Tools  May 21-22, 2014 •World Pharma Congress Boston, MA Program | Register | Download Brochure

nuclear receptors: Nuclear receptors are a super family of intra-cellular receptors present in most animal species. They mediate the transcriptional responses to metabolic ligands. In humans, 48 nuclear receptors have been identified. These are characterized as belonging to one of 11 subgroups. The most active targets are the estrogen receptors, glucocorticoid receptors, and progesterone receptors. Some 13% of drugs approved for sale in the United States are nuclear receptors with 15 of these drugs in the top 200 prescribed medicines. These top drugs represented $27.5 billion of sales revenue in 2009. The top-selling drug in this category is GlaxoSmithKline’s drug Advair/Seretide with sales of $7.8 billion in 2009. The major indications for these drugs include asthma, COPD, diabetes type II, hyperlipidemia, contraception, hormone replacement therapy, prostate cancer, and osteoporosis. Clearly nuclear receptors are an important class of targets for pharmaceutical development. Insight Pharma Reports Nuclear Receptors: The Pipeline Outlook  2010 See also orphan nuclear receptors, cytoplasmic and nuclear receptors

orphan G-protein-coupled receptors: GPCRs with unknown function.

orphan nuclear receptors: A broad category of receptor-like proteins that may play a role in transcriptional-regulation in the CELL NUCLEUS. Many of these proteins are similar in structure to known NUCLEAR RECEPTORS but appear to lack a functional ligand-binding domain, while in other cases the specific ligands have yet to be identified. MeSH 2010

orphan receptors: Receptor for which no ligands have yet been identified.  Related terms: deorphan, deorphanize

pharmacophores: The ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response. Does not represent a real molecule or a real association of functional groups, but a purely abstract concept that accounts for the common molecular interaction capacities of a group of compounds towards their target structure. Can be considered as the largest common denominator shared by a set of active molecules. This definition discards a misuse often found in the medicinal chemistry literature which consists of naming as pharmacophores simple chemical functionalities such as guanidines, sulfonamides or dihydroimidazoles (formerly imidazolines), or typical structural skeletons such as flavones, phenothiazines, prostaglandins or steroids. Pharmacophoric descriptors are used to define a pharmacophore, including H- bonding, hydrophobic and electrostatic interaction sites, defined by atoms, ring centers and virtual points. IUPAC Medicinal Chemistry

The ensemble of steric and electronic factors which are necessary to insure supramolecular interactions with a specific biological target structure. IUPAC Combinatorial Chemistry

A  template of chemical properties for an active site of a protein - representing these properties’ spatial relationship to one another - that theoretically defines a ligand that would bind to that site. 

pharmacophore generation: A procedure to extract the most important common structural  features relevant for a given biological activity from a series of molecules with a similar  mechanism of action. IUPAC Computational

phosphoinositide 3 kinase PI3K pathway:  The PI3K/Akt/mTOR signaling cascade serves many physiological and pathophysiological functions and is of major importance in a broad array of cancers. This has stimulated substantial interest in identifying and developing modulators of this pathway. The PI3K/Akt/mTOR Pathway November 2011Table of Contents | Tables and Figures |Executive Summary

promiscuous drugs: We contend that an ideal drug may be one whose efficacy is based not on the inhibition of a single target, but rather on the rebalancing of the several proteins or events, that contribute to the etiology, pathogeneses, and progression of diseases, i.e., in effect a promiscuous drug....  Corollaries to this argument are that the growing fervor for researching truly selective drugs may be imprudent when considering the totality of responses; and that the expensive screening techniques used to discover these, may be both medically and financially inefficient. Promiscuous drugs compared to selective drugs (promiscuity can be a virtue) Simon K Mencher and Long G Wang, BMC Clinical Pharmacology 2005, 5:3 doi:10.1186/1472-6904-5-3 http://www.biomedcentral.com/1472-6904/5/3/abstract  Related term: selectivity

promiscuous inhibitors: Nonspecific, seem to be hits in multiple high- throughput screening (HTS)  campaigns, but which turn out to be dead ends when attempts are made to optimise their activity, a key problem in the field of HTS.  Peter Kirkpatrick, Won't get fooled again, Nature Reviews Drug Discovery, 4(8): 630, August 2005  rotean ligands: The literature contains few examples of ligands that seem to be able to both promote and decrease activity at the same G-protein-coupled receptors. Such 'protean ligands' — so- called after the mythical character Proteus, who could adopt any shape he desired — have been proposed to work by acting as agonists with low efficacy. They thereby increase the activity of receptors that are basically silent under resting conditions, but decrease the activity of receptors that have high levels of ligand- independent, spontaneous (or constitutive) activity. In this model, protean behaviour therefore depends on having two populations of receptors with different levels of spontaneous activity. Adam Smith, Adrenoceptor pharmacology: How the ligand changed its spots Nature Reviews Drug Discovery 1, 569 Aug. 2002  http://www.nature.com/cgi-taf/Gateway.taf?g=5&file=/drugdisc/res_high/articles/nrd885.html&filetype=&_UserReference=

protease inhibitors:  Proteases constitute one of the largest potential drug target enzyme families, with 647 human gene products incorporating protease sequences and mutated proteases having been identified.  In addition, there are many more proteases found in viruses, bacteria, and parasites, which are also potential drug targets. The therapeutic promise of protease inhibitors has been most clearly demonstrated by angiotensin-converting enzyme (ACE) and HIV drugs.  Developments reviewed in this report indicate that more protease inhibitors, several having significant commercial potential, will reach the market over the next three to four years. Insight Pharma Reports, Protease inhibitors: Innovation drives drug pipeline, 2009 

Compounds which inhibit or antagonize biosynthesis or actions of proteases (ENDOPEPTIDASES) MeSH 1979

protein families, protein structure: Protein structure  Critical to determining whether a drug target is druggable

protein kinases: A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein. EC 2.7.1.37.  MeSH, 1980  Broader term: kinases Narrower terms: kinase inhibitors; -Omes & -omics kinome,  kinomics

protein kinase inhibitors: Agents that inhibit PROTEIN KINASES. MeSH 2005
Protein kinase evolution, SUGEN, 2002 http://www.kinase.com/evolution/

protein- protein interactions:
Protein-Protein Interactions April 23-24, 2014 • San Diego, CA Program | Register | Download Brochure
Protein-protein interactions (PPI) play a key role in many biological processes, making them promising targets for drug discovery. Though inhibition of protein-protein interactions has been challenging due to binding-site characteristics at the protein-protein interface, there has been considerable success in recent years.  

Disease-relevant intracellular protein-protein interactions occurring at defined cellular sites possess great potential as drug targets. They permit highly specific pharmacological interference with defined cellular functions. Drugs targeting such interactions are likely to act with fewer side effects than conventional medication influencing whole cell functions.  Protein-Protein Interactions as New Drug Targets Series: Handbook of Experimental Pharmacology, Vol. 186 Klussmann, Enno; Scott, John (Eds.) Springer 2008  http://www.springer.com/biomed/pharmaceutical+science/book/978-3-540-72842-9

Can be detected by yeast two- hybrids, phage display or immunoprecipitation assays.  John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html 

A central phenomenon determining the biological pathways found in living systems.  They are the focus of many proteomic technologies being developed today to decipher an intricate network of interactions. Correlated changes in protein expression (such as co- regulation or sequential regulation) provide a hint that two proteins may be interacting with each other. Play a major role in almost all relevant physiological processes occurring in living organisms, including DNA replication and transcription, RNA splicing, protein biosynthesis, and signal transduction.   Related terms: Proteomics  interaction proteomics, yeast two-hybrid.

protein targets: The purpose of the "PDB ligands" link is to give, at a glance, a quick way of determining if compounds in the selected SOM cluster have any "known" protein targets and if any homologous human proteins exist. The PDB ligands link from each cluster page provides connections to structural data as deposited in the Protein Data Bank (PBD). PDB Ligands Summary http://spheroid.ncifcrf.gov/spheroid/ManPages/ManPdbLigands.cfm  

proteomimetics-- small molecule:  The interaction between proteins is fundamental to many receptor- ligand, enzyme- substrate, and protein- protein interactions that have been linked to human disease states. Given the large number of novel protein targets emerging from the genome and the dearth of small molecules known to bind to and antagonize these targets, the challenge presented to the pharmaceutical industry is in the identification of novel agents effecting these novel targets. Traditional screening methods can be augmented by directed discovery efforts that seek to capture the essence of a protein's binding epitope in the context of a small molecule. Folding@home glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html  Related term: protein small molecule interactions  

proteonomics: Expression systems that can rapidly produce high levels of recombinant proteins are a critical link between the discovery of new genes and the identification of targets and molecules for drug development. Advances in the baculovirus expression technology makes it the system of choice in the emerging field of proteonomics where rapid production and high yields of biologically active complex proteins are essential in the discovery of new drug targets, vaccines, and biotherapeutics. Folding@home glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html   Related term: proteomics  

prototypes: First in class compounds usually directed at a specific molecular target. (Note that we have adapted the term for use in a broader sense to replace the term lead compound, which arguably loses some of its meaning after the4 lead optimization process.)  Insight Pharma Reports, Backup Compound Strategies: Best Practices for Reducing Phase II Risk, 2007

receptor: A protein or a protein complex in or on a cell that specifically recognizes and binds to a compound acting as a molecular messenger (neurotransmitter, hormone, lymphokine, lectin, drug, etc.). In a broader sense, the term receptor is often used as a synonym for any specific (as opposed to non- specific such as binding to plasma proteins) drug binding site, also including nucleic  acids such as DNA. IUPAC Computational  Narrower terms: amino acid receptors, cell surface receptors, drug receptors, receptor mapping In silico & Molecular modeling; Related terms:  Cell biology ligand; 

receptors, cytoplasmic and nuclear: Proteins in the cytoplasm or nucleus that specifically bind signaling molecules and trigger changes which influence the behavior of cells. The major groups are the steroid hormone receptors (RECEPTORS, STEROID), which usually are found in the cytoplasm, and the thyroid hormone receptors (RECEPTORS, THYROID HORMONE), which usually are found in the nucleus. Receptors, unlike enzymes, generally do not catalyze chemical changes in their ligands. MeSH 1994   See also nuclear hormone receptors 

receptor tyrosine kinase like orphan receptors: A family of cell surface receptors that were originally identified by their structural homology to neurotropic TYROSINE KINASES and referred to as orphan receptors because the associated ligand and signaling pathways were unknown. Evidence for the functionality of these proteins has been established by experiments showing that disruption of the orphan receptor genes results in developmental defects. MeSH 2010 

retargeting: A conceptual breakthrough in gene therapy would be gene transfer vector that could be systemically applied, allowing targeted gene transfer into a predetermined cell type.  C. Haynes et. al, Modified envelope glycoproteins to retarget retroviral vectors, Current Gene Therapy 3(5): 405- 410, Oct. 2003  Related term: Molecular Medicine gene therapy

selectivity: The word selectivity describes a drug's ability to affect a particular cell population in preference to others. As part of the current state of art in the search for new therapeutic agents, the property of selectivity is a mode of action thought to have a high degree of desirability....  Selectivity is generally a worthy property in a drug because a drug having high selectivity may have a dramatic effect when there is a single agent that can be targeted against the appropriate molecular-driver involved in the pathogenesis of a disease.  Promiscuous drugs compared to selective drugs (promiscuity can be a virtue) Simon K Mencher and Long G Wang, BMC Clinical Pharmacology 2005, 5:3 doi:10.1186/1472-6904-5-3 http://www.biomedcentral.com/1472-6904/5/3/abstract   Related term: promiscuous drugs

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target: Molecules in the body that may be addressed by drugs to produce a therapeutic effect. (Also used to refer to the material -- DNA or RNA - that one exposes to the probes on a microarray so that hybridization can be measured subsequently. A molecule that may interact with a drug or drug candidate. Pharmaceutical industry expert Jürgen Drews (now chairman of International Biomedicine Management Partners, Inc. and formerly of Hoffman La Roche) has noted that all drug therapy is currently based on 500 molecular targets.

Target in a drug screening context often means drug target. See also target (hybridization). Narrower terms: disease targets, gene target, tractable targetsRelated terms: drug targeting,  target validation

target amplification: Increasing the amount of target nucleic acid, providing more template for the label, to achieve improved detection. Useful for low levels of expression or abundance or very small sample sizes. Target amplification increases the amount of target nucleic acid, providing more template for the label and therefore more signal. This approach helps overcome problems associated with low expression of some genes or small sample sizes. The kinetics of the amplification step, however, must be reproduced exactly in these approaches; otherwise, changes observed on the array could be the result of differential amplification. Target- amplification processes include PCR, Rolling Circle Amplification RCA, Strand Displacement Amplification SDA.  Related terms: Gene amplification & PCR

target characterization: Requires evidence that the potential target actually plays a role in the disease process, and that modulation of the target may ameliorate or reverse a disease phenotype. A potential target which may be a validated target. Related terms:  target identification, target qualification, target validation  

target credentialing:
Identification of target molecules, evidence of modification of the target molecule, and measurement of desired effect. Clinical Radioresistance of Primary Glial Tumors, Radiation Biology, Progress Review groups, NINDS http://www.ninds.nih.gov/find_people/groups/brain_tumor_prg/RadiationBiology.htm 

There are now agents in clinical trial or about to enter clinical trial that have been designed against a specific molecular target. The putative target for a number of these agents has also been associated with radioresistance. Such agents will be evaluated for their ability to modify tumor cell radiosensitivity. Critical to these studies will be the establishing a causal relationship between the agent-induced modification of the target and radiosensitization. This will serve to validate (or invalidate) a given molecule as a target for radiosensitization (target credentialing) and establish a "marker" for the use in the potential design of a clinical trial. Although initial studies will be performed using tumor cell lines and normal cells in vitro, agents found to be effective in vitro will then be evaluated using in vivo models.  Molecular Radiation Therapeutics Branch, National Cancer Institute http://www3.cancer.gov/rrp/mrtb.html 

target evaluation:
The shift from traditional to genomics-and proteomics-based drug discovery has fundamentally changed the way researchers view the subject of targets. After decades of focusing on a few hundred relatively well-characterized therapeutic targets, drug developers are now finding that the genomics revolution has presented them with the opposite dilemma: thousands of prospective targets about which little is known. Insight Pharma Reports, Powering Discovery through Target Evaluation: Moving beyond the validation paradigm, 2005 http://www.insightpharmareports.com/reports/2005/52_TargetValidation/overview.asp 

Can cover the range of target- winnowing strategies, from target identification to target validation.   

target families/target family:  The majority of pharmaceutically relevant drug targets cluster into densely populated target families, thus offering a novel approach that complements the currently favoured screening paradigm in medicinal chemistry. This approach uses a privileged structure concept whereby molecular masterkeys are developed that account for a target family wide structural or functional commonality. Numerous lead compounds, based on multipurpose privileged structures, can be generated that address a variety of targets from a gene family of interest, irrespective of therapeutic area. Medicinal  chemistry of targeted directed masterkeys, Drug Discovery Today, 2003 http://www.ncbi.nlm.nih.gov/pubmed/12927511 

Although the sheer numbers of potential targets uncovered through genomics- based methods create an enormous need for target- identification and validation technologies, these numbers also make possible new opportunities, which go way beyond what is possible via traditional drug discovery methods. The limited number of target families addressed by traditional drug discovery methods suggests that these methods are "boxed in" and unable to create the numbers of novel drugs (three to five per year for major companies) that will be necessary to meet pharmaceutical companies' business goals. 

target gene families:  small molecule leads — identified by virtue of their interaction with a single member of a gene family — are used to study the biological role of other members of that family, the function of which is unknown. Chemogenomics: an emerging strategy for rapid target and drug discovery, Markus Bredel & Edgar Jacoby, Nature Reviews Genetics 5, 262-275 April 2004  http://www.nature.com/nrg/journal/v5/n4/box/nrg1317_BX1.html  See also Chemistry chemogenomics  

target glut:  While an individual company may have four or five times as many targets under analysis now than it did five years ago, most of those targets are completely new or poorly understood. Lack of annotation for genomic data is a major problem in choosing the best targets to pursue for drug developmentRelated terms:  target identification, target screening, target validation; Bioinformatics: information overload; Drug discovery & development druggable genome

target haplotype: Pharmacogenomics

target hopping: Directed crossover of a compound to a new target. "Chemical genomics advances drug discovery" Genetic Engineering News 22 (13):1 , July 2002 www.messebasel.ch/miptec/ .%5Cpdf%5CGEN_July_Aldridge.pdf   Related term?:  Assays lead hopping  Chemistry scaffold hopping 

target (hybridization): 
There are currently at least two nomenclature systems for referring to hybridization partners. Both use common terms ‘probes’ and ‘targets’ … With respect to the nucleic acids whose entwining represents the hybridization reaction, the identify of one is defined - it tends to be tethered to the solid phase, making up the microarray itself. The identity of the other is revealed by hybridization. The strategy of the ‘standard’ microarray therefore parallels that of a reverse dot- blot, in which the probe is immobilized. For this reason, authors of articles appearing in this supplement have been encouraged to describe the tethered nucleic acid as ‘probe’ and the free nucleic acid as ‘target’. Chipping Forecast supplement "A note on nomenclature" Nature Genetics 21 (1s): 1 Jan 1999 Has this been standardized yet?  See also the note under probes- microarray Microarrays

A molecule (usually a protein gene product, but sometimes a DNA sequence, or, in the case of antisense drugs, an mRNA) that may interact with a drug or drug candidate.  Instead of target, some people use sample [in the context of microarrays] . We find fault with this usage, though we fall into it occasionally, because the same word often refers to the biological material from which mRNA was extracted (e.g., tissue or serum from patients or laboratory animals). In addition, sample is an important term in statistics, where it has a completely different meaning. (It means the subset of a population that is surveyed for the purpose of estimating properties of the entire population.). 
See also target
[above] Related terms: Drug discovery & development Sample and sample preparation 

target identification:  Knowing the cellular targets of drugs is crucial if the process of drug discovery is to be made more efficient. Identifying the full spectrum of targets associated with a bioactive small molecule can lead to faster optimization, understanding of off-target side effects and the ability to minimize possible toxicities early on in the process.. Target Identification, Whitehead Institute http://www.broadinstitute.org/scientific-community/science/platforms/proteomics/target-identification

Target identification of biologically active molecules such as natural products, synthetic small molecules, peptides, and oligonucleotides mainly relies on affinity chromatography, activity-based probes, or photoaffinity labeling (PAL). Amongst them, activity-based probes and PAL have offered great advantages in target identification technology due to their ability to form covalent bonds with the corresponding targets. Activity-based probe technology mainly relies on the chemical reactivity of the target proteins, thereby limiting the majority of the biological targets to enzymes or proteins which display reactive residues at the probe-binding site. Molecules 2013, 18(9), 10425- 10451;  doi:10.3390/molecules180910425 Review  Recent Advances in Target Characterization and Identification by Photoaffinity Probes Jitapa Sumranjit 1,2 and Sang J. Chung http://www.mdpi.com/1420-3049/18/9/10425

Identifying molecules that clearly play a role in a disease process. Target identification methods  provide a finer degree of detail than target screening and require evidence that the gene/ protein is correlated with the disease.   

target labelling: Targets for arrays are labelled representations of cellular mRNA pools. Typically reverse transcription from an oligo-dT primer is used … Frequently total RNA pools (rather than mRNA selected on oligo-dT) are labelled, to maximize the amount of message that can be obtained from a given amount of tissue.  DJ Duggan et al “Expression profiling using cDNA microarrays” Nature Genetics 21(1s): 10- 14, Jan 1999  

target molecules: Target genes or target proteins.  

target prioritization:  Target prioritization is today a bottleneck as a result of the new genomics based drug discovery. Given the exponential increase in targets provided by the new technologies as gene expression analysis, no company can afford to advance all of the targets identified. Our Markets: The Drug Discovery Industry, InNetics http://innetics.com/markets.htm 

target prioritization TDR database http://tdrtargets.org/ The TDR Targets project seeks to exploit the availability of diverse datasets to facilitate the identification and prioritization of drugs and drug targets in neglected disease pathogens.

target product profiles:
A tool for planning in the development phase of R&D projects. Insight Pharma Reports, Backup Compound Strategies: Best Practices for Reducing Phase II Risk, 2007 

target proteins:  The project TargId at GMD SCAI focuses on methods to address the arguably most urgent problem: the elucidation of the origins and mechanisms of human diseases, culminating in the identification of potential drug target proteins. Identification of Drug Target Proteins, by Alexander Zien, Robert Küffner, Theo Mevissen, Ralf Zimmer and Thomas Lengauer ERCIM News No.43 - October 2000  http://www.ercim.org/publication/Ercim_News/enw43/zien.html 

target qualification:
Qualifying that potential target genes or proteins clearly have a role in a disease process.

target screening: Identifying molecules that may be associated with a disease process (e.g., upregulation of a particular gene identified through gene expression analysis). CHA, Cambridge Healthtech Advisors Model Animal Systems: Emerging Applications and Commercial Opportunities in Drug Discovery and Development, report, 2004  Related terms: target glut, target identification, target validation  

target selection: The main purpose of the Bioinformatics Core (BIC) is to select the target for research. The goals of BIC are to develop complete high throughput technology for structural genomics beginning with high throughput computational selection of target proteins, followed by robotic expression and crystallization and fully automated data collection and structure solution. List of Important Definitions, JCSG Joint Center for Structural Genomics http://www.jcsg.org/help/robohelp/Definitions/Target_Selection.htm   http://www.nigms.nih.gov/News/Reports/psi_targetselect.htm 

target space: Structure-Based Drug Design (SBDD) has been in use within the pharmaceutical industry for over twenty-five years. SBDD continues to play an important role in drug discovery, design and optimization. Moreover, with the development of sophisticated biophysical and computational methodologies SBDD is impacting hit identification and ‘hit to lead’ optimization approaches across the industry.  Therapeutic Target Space DVD 2010  

target validation:  The identification and validation of disease-causing target genes is an essential first step in drug discovery and development. Genomics and proteomics technologies have already begun to uncover novel functional pathways and therapeutic targets in several human diseases such as cancers and autoimmunity. Also, bioinformatics approaches have highlighted several key targets and functional networks. In contrast to gene-profiling approaches, phenotype-oriented target identification allows direct link between the genetic alterations and a disease phenotype. Therefore, identified genes are more likely to be a cause rather than a consequence of the disease. Once a gene target or a mechanistic pathway is identified, the next step is to demonstrate that it does play a critical role in disease initiation, perpetuation, or both. Methods Mol Biol. 2007;360:1-12. Main approaches to target discovery and validation. Sioud Mhttp://www.ncbi.nlm.nih.gov/pubmed/17172722

Target validation involves 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, 2004

Determining which among genes or proteins being investigated as potential drug targets lead to phenotypic changes when modulated, suggesting that they may have value as therapeutic targets. Many people would say a target is truly validated only after proven effective in human trials.  The definition of target validation is clearly evolving, can be seen as "slippery" and clearly means different things to different people.  

target validation technologies: A range of strategies exists for modulating gene expression in vitro and in vivo. These strategies include the use of antibodies, negative dominant controls, antisense oligonucleotides, ribozymes, and small-interfering RNAs. In contrast to in vitro assays, mouse reverse genetics such as knockout phenotypes has become a powerful approach for deciphering gene function and target validation in the context of mammalian physiology. In addition to disease-causing genes, the identification of antigens that stimulate both arms of the immune system is the major goal for effective vaccine development.  Methods Mol Biol. 2007;360:1-12. Main approaches to target discovery and validation. Sioud Mhttp://www.ncbi.nlm.nih.gov/pubmed/17172722

A number of technologies including downregulation of gene expression (gene knockdown, antisense, ribozymes and zinc finger proteins), protein inhibition (phage libraries and antibodies), cellular assays, chemical genetics, and combinatorial biology are linked with target validation. The integration of various technologies is another challenge.

targeted gene repair: A technique which uses synthetic oligonucleotides to direct the cell's inherent DNA repair system to correct a mutation at a specific site in an episome or chromosome.
MeSH 2007

targeted therapy: A type of treatment that uses drugs or other substances capable of interfering with targeting molecules that are needed for carcinogenesis and tumor growth. The benefit of targeted therapy is that cancer cells are attacked without harming normal cells.  TARGET Therapeutically Applicable Research to Generate Effective Treatments , National Cancer Institute Glossary http://target.cancer.gov/resources/glossary/ 

The goal of targeted therapeutics is to create drugs that by the specificity of their design and delivery will make them more effective in treating disease and less toxic.
Therapeutic Targets Database:
http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp  Computational Science Dept, Science Faculty, National University of Singapore 

tractable targets:  Targets from families such as 7TM receptors, ion channels, kinases and proteases which have produced previous hits.  Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5(7): July 2000  Related terms: druggable, low hanging fruits, pharmaceutically tractable 

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ubiquitin pathway: Drugs targeting the ubiquitin system are still relatively new; the first approval by the FDA happened in 2003. Ubiquitination (ligases) as well as deubiquitination (deubiquitylating enzymes (DUB’s) play key roles in cellular signal transduction pathways and offer numerous opportunities for therapeutic interventions for treating diseases such as cancer, inflammation and metabolic diseases. However, in order to bring more ubiquitin targeting drugs to the market, some challenges need to be addressed. Targeting the Ubiquitin Pathway October 1-2, 2012 • Boston, MA Program | Register | Download Brochure Targeting the Ubiquitin Pathway

virtual target screening: Computational methods involving virtual screening could potentially be employed to discover new biomolecular targets for an individual molecule of interest (MOI). However, existing scoring functions may not accurately differentiate proteins to which the MOI binds from a larger set of macromolecules in a protein structural database. An MOI will most likely have varying degrees of predicted binding affinities to many protein targets. However, correctly interpreting a docking score as a hit for the MOI docked to any individual protein can be problematic. In our method, which we term "Virtual Target Screening (VTS)", a set of small drug-like molecules are docked against each structure in the protein library to produce benchmark statistics. This calibration provides a reference for each protein so that hits can be identified for an MOI. VTS can then be used as tool for: drug repositioning (repurposing), specificity and toxicity testing, identifying potential metabolites, probing protein structures for allosteric sites, and testing focused libraries (collection of MOIs with similar chemotypes) for selectivity. J Chem Inf Model. 2012 Aug 27;52(8):2192-203. doi: 10.1021/ci300073m. Epub 2012 Jul 23. Virtual target screening: validation using kinase inhibitors. Santiago DNPevzner YDurand AATran MScheerer RRDaniel KSung SSWoodcock HLGuida WCBrooks WHhttp://www.ncbi.nlm.nih.gov/pubmed/22747098

Bibliography
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions. http://www.chem.qmw.ac.uk/iupac/bioinorg/
IUPAC Glossary of Terms used in Biomolecular Screening, IUPAC Recommendations 2011  http://iupac.org/publications/pac/83/5/1129/
IUPAC International Union of Pure and Applied Chemistry, Glossary of Medicinal Chemistry, Part II (IUPAC Recommendations 2013) http://pac.iupac.org/publications/pac/pdf/2013/pdf/8508x1725.pdf
MeSH Medical Subject Headings, (PubMed Browser) National Library of Medicine, Revised annually.  250,000 entry terms, 19,000 main headings. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=MeSH&term= 

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