Genomic biology & chemistry Map:  Finding guide to terms in these glossaries  Site Map
Related glossaries include Applications: Drug discovery & development   Drug targets   Metabolic engineering  Pharmacogenomics  
Informatics: Cheminformatics  In silico & molecular modeling glossary
Technologies: Assays & screening  Combinatorial libraries & synthesis   Labels, signaling & detection  Mass spectrometry  Microarrays   Miniaturization & nanoscience 
Biology: Expression  Nomenclature  Pharmaceutical biology & chemistry

backup compounds: Heads of R&D and chemistry, therapeutic area heads, portfolio analysts, and project managers all recognize that there is no surer way to minimize Phase II risk than a well thought-out backup plan. This report drives home real world experiences and best practices in backup compound strategies. Insight Pharma Reports, Backup Compound Strategies: Best Practices for Reducing Phase II Risk, 2007

biochemical genomics: We have recently developed a biochemical genomics approach to identify genes by the activities of their products, together with Stan Fields (Univ. Washington) and E. Grayhack. To this end, we first constructed a library of ca. 6000 strains, each of which expresses a unique yeast ORF as a GST- ORF fusion. To identify genes encoding different activities, the GST- ORFs are purified in pools, activity is assayed, and active pools are deconvoluted to determine the GST- ORF responsible for activity. Using this approach we have linked three previously unknown gene products with specific biochemical activities. [MR Martzen et al University of Rochester, US “A biochemical genomics approach for identifying genes by the activity of their products. Science 286: 1153-155, 1999]  http://www.urmc.rochester.edu/gebs/faculty/eric_phizicky.htm 

Related terms: chemical genomics, chemogenomics

biochemical networks, biochemical pathways, biochemical systems theory: Metabolic profiling

biochemistry, medical: Michael W. King, Indiana Univ. School of Medicine, 1996- 2004 http://web.indstate.edu/thcme/mwking/home.html 

biological chemistry: A multi-disciplinary area with strong links to fundamental molecular and mechanistic topics. These topics are essential for the progress in the field. IUPAC shall be visible and shall have a central role in efforts to support strong links between chemistry and biology. ...Informal discussions at the Beijing GA resulted in a proposal to establish contacts with interested partners within IUPAC to form an informal discussion forum for the coordination and promotion of activities within the area of biological chemistry.  ...  The project will stimulate contacts and interactions between scientists who are active in the field. The aim of the project is to make an inventory and a feasibility study in order to present some proposals for IUPAC activities within this area.  IUPAC,  Chemistry for Biology - an inventory of interdivisional and interdisciplinary activities within IUPAC in the field of biological chemistry, 2006  http://www.iupac.org/projects/2005/2005-042-1-300.html 

biologically relevant chemical space: Those parts of chemical space in which biologically active compounds reside. Christopher M. Dobson, "Chemical space and biology" Nature 432 (7019): 824- 828, Dec. 16, 2004

Broader term: chemical space

bioorganic chemistry: includes topics such as enzymic and enzyme- like catalysis, protein/ enzyme structure-function relationships, enzyme cofactor chemistry and biochemistry, nucleic acid chemistry and biochemistry, bioconjugates, bioprobes, and molecular recognition. Bioorganic & Medicinal Chemistry, Univ. of Oregon, Chemistry Dept. http://www.uoregon.edu/~chem/bioorg.html

characterization: Biomolecules glossary

chemical biology:  The purpose of ACS Chemical Biology is to provide an international forum for the rapid communication of research that broadly embraces the interface between chemistry and biology. ... Results will be published in which molecular reasoning has been used to probe questions through in vitro investigations, cell biological methods, or organismal studies. We welcome mechanistic studies on proteins, nucleic acids, sugars, lipids, and non-biological polymers. The journal serves a large scientific community, exploring cellular function from both chemical and biological perspectives. American Chemical Society, journal scope note http://pubs.acs.org/journals/acbcct/about.html 

Related term: chemical genomics

chemical biomarkers: Biomarkers glossary

chemical cytometry: Ultrasensitivity glossary

chemical cleavage sequencing, chemical degradation sequencing: See Sequencing glossary  Maxim- Gilbert sequencing.

chemical genetics: A "chemistry first" approach to drug discovery. Chemical genetics strategies start with libraries of chemical compounds, and then screen these libraries to find compounds that produce differences in a disease- relevant phenotype. Once a phenotype modifying compound is found, it is used to identify the particular target protein to which it binds in the cells or small model organisms in which it had previously been studied.  Sometimes used interchangeably with "chemical genomics".  CHA, Cambridge Healthtech Advisors Model Animal Systems: Emerging Applications and Commercial Opportunities in Drug Discovery and Development, report, 2004

As the term has traditionally been used, has referred to studies that uncover the genetically controlled pathways influenced by a single specific compound. Also used to describe a method pioneered by Stuart Schreiber (Harvard Medical School, Howard Hughes Medical Institute involving a phenotypic screen employing a vast library of small molecules that have been introduced into a cellular assay. ...  The coverage of such studies can be genomic, but the detailed activity information they provide is at the genetic level (one gene within a particular pathway) http://www-schreiber.chem.harvard.edu 

"Chemical genetics approach" first coined [by Rebecca Ward, at Harvard University] on the inaugural cover of Chemistry and Biology nine years ago. Her term reminds us that to understand a life process you should perturb it and determine the consequence and that such an approach should strive to have the broad power and generality of  genetics. Stuart L. Schreiber, The Small Molecule Approach to Biology, Chemical & Engineering News, March 3, 2003 http://www-schreiber.chem.harvard.edu/home/pdffiles/8109genomics.pdf

Related terms: chemical genomics, chemogenomics

chemical genomics:  The targets of many drug candidates are unknown and are often difficult to tease out from among the thousands of gene products found in a typical organism. The “blindness” in the welter of potential cellular targets means that the process of designing therapeutic drugs is neither precise nor efficient. The exploration of chemical genomics will transform our understanding of how the human genome and proteome function. CHEMICAL GENOMICS: Small Molecules to Discover Targets, Discovery on Target, Oct 24-25, 2006 • Boston, MA

Related/near synonymous? terms: chemical genetics, chemical genomics

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] %20screening%20in%20drug%20discovery.pd

chemical markup language CML: Cheminformatics glossary

chemical microarrays: Microarrays categories

chemical proteomics:   Makes use of synthetic small molecules that can be used to covalently modify a set of related enzymes and subsequently allow their purification and/or identification as valid drug targets. Furthermore, such methods enable rapid biochemical analysis and small- molecule screening of targets thereby accelerating the often difficult process of target validation and drug discovery.  DA Jeffery, M. Bogyo, Chemical proteomics and its application to drug discovery, Current Opinion in Biotechnology 14(1): 87-95, Feb. 2003

Uses labelled- irreversible protease inhibitors to isolate or identify active proteases in complex mixtures by two- dimensional (2D) gel electrophoresis or by using protease-activity chips with matrix- assisted laser desorption- ionization– time- of- flight (MALDI– TOF) or MALDI– quadrupole– TOF (MALDI– Q– TOF) mass- spectrometric identification of the captured proteases. In vivo applications of activity inhibitor probes include determination of protease function by chemical knockouts or intravital imaging of proteolytic activity. Protease Degradomics: A New Challenge for Proteomics, Carlos Lopez- Otin & Christopher M. Overall, Nature Reviews Molecular Cell Biology 3, 509 -519 (2002)
http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrm/journal/v3/n7/abs/nrm858_r.html

To link new proteins with known catalytic activities, proteome- scale screens for generic enzyme activities (e.g. protease and phosphatase) should be implemented ... Although it is impossible to screen for chemical reactions that are unknown, in theory, identifying small molecules that bind to the new proteins may elucidate clues to new activities. These ligands might be found by screening the new proteins against diverse chemical libraries using existing methods such as NMR spectroscopy, microcalorimetry, or microarrays. The general concept of ascribing function to new proteins by discovering small molecule ligands might be referred to as chemical proteomics. Aled Edwards et al. “Proteomics: new tools for a new era” Modern Drug Discovery 3 (7): 35- 44 Sept. 2000   http://pubs.acs.org/journals/mdd/toc/0900toc.html

Related term/equivalent?: chemiproteomics

Google= about 708 July 15, 2004; about 17.500 Aug 1, 2007

chemical self-assembly: Biomaterials glossary

chemical shift: NMR & x-ray crystallography glossary

chemical space: The heartland of this debate [about how many samples are enough] centres on the definition, and hence extent, of chemical space. More precisely, it focusses on the extent of chemical space that is accessible by chemical synthesis and which could be described as drug- like. [Martin J. Valler,  Darren Green  "Diversity screening versus focussed screening in drug discovery " Drug Discovery Today 5(7): July 2000

Encompasses all possible small organic molecules, including those present in biological systems--is vast. So vast, in fact, that so far only a tiny fraction of it has been explored. ... A term often used in place of 'multi- dimensional descriptor space'; it is a region defined by a particular choice of descriptors and the limits placed on them. In the context of this insight, chemical space is defined as the total descriptor space that encompasses all the small carbon -  based molecules that could in principle be created. Christopher M. Dobson, "Chemical space and biology" Nature 432 (7019): 824- 828, Dec. 16, 2004

Narrower term: biologically relevant chemical space. Related term:  property space

chemiexcitation, chemiluminescence: Labels, signaling & detection glossary 

chemiproteomics: Identifying the mode of action and evaluating the specificity of new lead compounds are essential and critical steps in the preclinical drug development process. However, in many cases the mode of action of active compounds cannot be easily assessed in complex cell-based screening systems Prolexys Pharmaceuticals, 2007 http://www.prolexys.com/secondary.php?pageId=42 

Google = about 254 July 15, 2004, about 219 Aug 1, 2007

Related term/equivalent?: chemical proteomics

chemogenomics: There is some confusion about the meaning of the term 'chemogenomics'¹⁰³; this might be expected given the involvement of so many disciplines. In particular, there is considerable overlap among the related strategies described by the terms 'chemical genetics'¹⁰⁴ and 'chemical genomics'^{105, 106}. Although these three terms are sometimes used interchangeably, the primary goal of both of the last two strategies is the study of cellular function using small synthetic molecules as modulating ligands.  By contrast, the term 'chemogenomics' is often used to describe the focused exploration of target gene families, in which 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. Box 1 Defining chemogenomics from the following article: Chemogenomics: an emerging strategy for rapid target and drug discovery, Markus Bredel & Edgar Jacoby, Nature Reviews Genetics 5, 262-275 April 2004 doi:10.1038/nrg1317

Sometimes referred to as chemical genomics. was most likely first used by Vertex Pharmaceuticals to describe its parallel drug design approach, which involves using structures of proteins in a given family to design drugs for the family as a whole.  The Vertex approach is truly parallel (i.e., involving multiple targets at once) and combines structural biology, biased library design and screening, and structure- based drug design. At its limit, chemogenomics represents the discovery and description of all possible compounds that can interact with any protein encoded by the human genome. The term chemogenomics is slowly (and somewhat grudgingly) catching on.  Broadly, it now appears to mean “taking a combinatorial approach to screening protein targets by family/ class.” Detailed protein structure information is used to design libraries that are “biased” to contain compounds that are more likely to interact with a particular protein family (hence, it is a “genomic” approach).  This screening methodology helps researchers identify the best small molecule compound to bind to a target (hence it is a “chemical” approach).

Related, (near) synonymous terms: chemical genomics, chemical genetics Narrower terms: functional chemogenomics, structural chemogenomics; In silico & Molecular modeling glossary  in silico chemical genomics

chemistry & drug discovery: 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.  CHI’s Drug Discovery and Development Map

chemotype: A group of organisms that produce the same profile for a particular class of chemicals such as chalcones, aurones, flavanols, etc. Vernon V. Vandiver, Jr. Aquatic Weed Terms, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida http://edis.ifas.ufl.edu/BODY_AG007.html 

computational chemistry:  A discipline using mathematical methods for the calculation of molecular properties or for the simulation of molecular behavior.  It also includes, e.g., synthesis planning, database searching, combinatorial library manipulation (Hopfinger, 1981; Ugi et al., 1990). [IUPAC Computational]

Computational chemistry seeks to predict quantitatively molecular and biomolecular structures, properties, and reactivity by computational methods alone. It uses modern chemical theory to predict the speed of unknown reactions and the synthetic sequences by which complex new molecules can be made most efficiently. Computational chemistry allows chemists to explore how things work at the atomic and molecular levels and to draw conclusions that are impossible to reach by experimentation alone. Thus, computational chemistry supplements experimentally derived data. Gary D. Wiggins, "What is Chemical Informatics?"  Indiana Univ., US, 2006 http://www.chembiogrid.org/resources/whatis.html  

Related terms: In silico & molecular modeling glossary Computer Aided Molecular Design CAMD, molecular graphics

 Drug Discovery Chemistry April 28-30, 2008 • La Jolla, California includes  Fragment-Based Drug Discovery   G-Protein Coupled Receptor Drug Discovery   Protein Protein Interactions as drug targets   Tools and technologies for fragment based design 

dyes, electrochemistry, electrochemiluminescence, electronic nose: Labels, signaling & detection glossary 

fine chemicals: Pure, single substances that are produced by chemical reactions and are bought and sold on the basis of their chemical identity. Pharmaceutical fine chemicals include both intermediates for drug production and bulk active drugs ready to be compounded with inert pigments, solvents, and fillers -- called excipients -- and made into dosage forms. The combination of fine chemicals and performance chemicals makes up the group called specialty chemicals. As opposed to fine chemicals, performance chemicals are often mixtures of substances, proprietary products, formulated with carriers or solvents, and bought and sold for what they do. What are fine chemicals? Pharmaceutical Fine Chemicals, Chemical & Engineering News, July 10, 2000  http://pubs.acs.org/cen/coverstory/7828/7828spec.html#Anchor-1344 

fluorous chemistry: Highly fluorinated chemical moieties are attached to small organic compounds to facilitate purification of the desired products of a chemical reaction. D Evanko, Chemical Tools,  Nature Methods 2(6):406-507 

forward chemical genetics: Involves identifying a phenotype in an organism or cell caused by a small molecule and then identifying the target affected. In principle this is analogous to a classical genetics screen, in which one screens for a mutation that has a desired phenotype and then identifies the mutant gene that is responsible. ...  Forward chemical genetics was an extremely powerful tool in the early days of drug discovery, and we expect that it will be equally powerful if applied systematically to basic biology. Biology Overview Initiative for Chemical Genetics, Institute of Chemistry and Cell Biology, Harvard Medical School, US  http://iccb.med.harvard.edu/biology/ 

Related terms: reverse chemical genetics;  Genetic manipulation & disruption glossary forward genetics, forward genomics

fragment based drug discovery:  The fragment-based approach to drug design has potential for efficient progression into clinically successful compounds. Library design and computational ligand modeling to identify potential fragments, initial screening techniques, molecular optimization based on ligand/target characterization, linking, biological screens, and morphing- scaffold hopping will be explored to identify advances to meet the challenges in the process.  Fragment- Based Drug Discovery  Drug Discovery Chemistry April 28-30, 2008 • La Jolla, California 

G protein coupled receptors: Drug targets glossary

green chemistry: The terminology "green chemistry" or "sustainable chemistry" is the subject of debate. The expressions are intended to convey the same or very similar meanings, but each has its supporters and detractors, since "green" is vividly evocative but may assume an unintended political connotation, whereas "sustainable" can be paraphrased as "chemistry for a sustainable environment", and may be perceived as a less focused and less incisive description of the discipline. Other terms have been proposed, such as "chemistry for the environment" but this juxtaposition of keywords already embraces many diversified fields involving the environment, and does not capture the economic and social implications of sustainability. The Working Party decided to adopt the term green chemistry for the purpose of this overview. This decision does not imply official IUPAC endorsement for the choice. In fact, the IUPAC Committee on Chemistry and Industry (COCI) favors, and will continue to use sustainable chemistry to describe the discipline. Special Topic Issue on Green Chemistry, Pure Appl. Chem., Vol. 72, No. 7, pp. 1207-1228, 2000 http://www.iupac.org/publications/pac/2000/7207/7207tundo.html

heterodimer: Biomolecules glossary

high throughput chemistry: Ten years ago, combinatorial chemistry began emerging as a highly efficient means of generating as many compounds as desired, feeding the demand for compounds as a result of increasingly high throughput screening.  Now there is growing recognition of the need for greater quality and diversity over sheer numbers, and greater experience is making it possible to more intelligently design better libraries. 

immunohistochemistry: Labels, signaling & detection glossary 

in silico chemical genomics: In silico & molecular modeling glossary

isomer: Biomolecules glossary

materials chemistry: The last 10-15 years have seen the emergence and rapid growth of 'materials chemistry' as a distinct discipline within the broad family of chemical sciences. This was a combination of noun and adjective that had not previously formed part of the chemists' vocabulary. Now a significant fraction of all publications in chemistry claim to form part of this new field. In particular two international journals (Chemistry of Materials, published by the American Chemical Society and the Journal of Materials Chemistry, published by the Royal Society of Chemistry in Great Britain) are achieving high impact factors and publish work emanating from every continent of the world. Yet there remains no definition of the phrase 'materials chemistry' agreed by the global chemical community. IUPAC, Towards defining materials chemistry, 2005, project number: 2005-001-1-200 http://www.iupac.org/projects/2005/2005-001-1-200.html

medicinal chemistry: A chemistry based discipline, also involving aspects of biological, medical and pharmaceutical sciences. It is concerned with the invention, discovery, design, identification and preparation of biologically active compounds, the study of their metabolism, the interpretation of their mode of action at the molecular level and the construction of structure- activity relationships [IUPAC Medicinal Chemistry

 Mastering Medicinal Chemistry Molecular Medicine Triconference, March 25-28, 2008, San Francisco CA 

Focuses on designing new types of drug molecules utilizing cutting edge techniques such as combinatorial chemistry, computer- aided molecular design, and new types of highly sophisticated receptor-based and cell biological assays for drug activity. In addition, the more traditional areas of lead compound development through molecular modification and the use of quantitative structure activity relationships (QSAR) still play an important role in medicinal chemistry. Bioorganic & Medicinal Chemistry, Univ. of Oregon, Chemistry Dept. http://www.uoregon.edu/~chem/bioorg.html

What's medicinal chemistry? Combinatorial Chemistry Initiative, Univ. of Buffalo, SUNY, US http://wings.buffalo.edu/academic/department/pharmacy/mch/public_html/whats.html

Wikipedia http://en.wikipedia.org/wiki/Medicinal_chemistry 

Google = about 238,000 June 21, 2004; about 1,540,000 Nov 13, 2006

Narrower term: dynamic medicinal chemistry

medicinal systems biology: This review will focus on the development of a novel "chemical genetic/ genomic approach" that uses small molecules to "probe and identify" the function of genes in specific biological processes or pathways in human cells. Due to the close relationship of small molecules with drugs, these systematic and integrative studies will lead to the "medicinal systems biology approach" which is critical to "formulate and modulate" complex biological (disease) networks by small molecules (drugs) in human bio-systems. TK Kim, Chemical genomics and medicinal systems biology: chemical control of genomic networks in human systems biology for innovative medicine, J Biochem Mol Biol. 37(1): 53- 58, Jan 31, 2004

Google = about 16 June 21, 2004; about 214 Nov 12, 2007

microchemical systems, microchemistry: Miniaturization & nanoscience glossary

molecular scaffold: The molecular scaffold is an oft-cited concept in medicinal chemistry suggesting that the definition of what makes a scaffold is rigorous and objective. However, this is far from the case with the definition of a scaffold being highly dependent on the particular viewpoint of a given scientist.  N Brown, E Jacoby, On scaffolds and hopping in medicinal chemistry. Mini Rev Med Chem 6 (11) :1217- 1229, Nov 2006.

Related term: scaffold hopping

NCE New Chemical Entity: Drug approvals glossary

natural products:  http://en.wikipedia.org/wiki/Natural_products 

Revised Section F Natural products and related compounds IUPAC, Commission on Nomenclature of Organic Chemistry, 1999 Recommendations P.M. Giles, Jr. Pure Appl. Chem., 1999, 71, 587-643.http://www.chem.qmw.ac.uk/iupac/sectionF/ 

Related terms: Biomaterials glossary biomimetic materials, biomimetics

nanochemistry: Miniaturization & nanoscience glossary

organic chemistry:  The role played by organic chemistry in the pharmaceutical industry continues to be one of the main drivers in the drug discovery process. However, the precise nature of that role is undergoing a visible change, not only because of the new synthetic methods and technologies now available to the synthetic and medicinal chemist, but also in several key areas, particularly in drug metabolism and chemical toxicology, as chemists deal with the ever more rapid turnaround of testing data that influences their day- to- day decisions. M MacCoss, TA Baillie, Organic chemistry in drug discovery, Science 303 (5665): 1810- 1813, Mar. 19, 2004

Organic electronics, Advanced Technology Program ATP, NIST National Institute of Standards and Technology http://www.atp.nist.gov/oet/oet_off.htm 

PAT Process Analytical Technology: Chemistry glossary

patent literature and chemical structures: Intellectual property & legal glossary

peptidomimetic: A compound containing ono- peptidic structural elements that is capable of mimicking or antagonizing the biological action (s) of a natural parent peptide. A peptidomimetic does no longer have classical peptide characteristics such as enzymatic ally scissile peptic bonds. [IUPAC Medicinal Chemistry]

Peptides are highly flexible, a quality that counteracts their receptor-affinity. Peptides are degraded by proteases in the stomach and should be administered intravenously. In the blood peptides are degraded by proteases as well and cleared from the circulation rapidly. Peptides are often too water-soluble to be able to pass the barriers that separate them from their targets in the cells and in the brain. All these disadvantages prevent peptides from becoming drugs and stimulate the quest for peptide mimics.  ... Peptidomimetics are often more stable than peptides and less easily cleared from the blood stream. Peptidomimetics, PepScan Systems  http://www.pepscan.nl/html/outframeset.html

Related terms: Omes & omics glossary peptidome, peptidomics

peptidomics: -Omes & -omics glossary

performance chemicals: See under fine chemicals

photochemistry: Molecular imaging glossary

post-genomic chemistry: Knowledge of human genome and of those of other organisms creates number of new avenues for natural sciences. The main aim of the proposed project is to analyze present and future impact of information yielded by functional genomics on the modern chemistry and bioorganic chemistry in particular. Specific working panels will be assembled to analyze and discuss the following topics: Post-genomic strategies for drug design, Protein chemistry, sequence - structure - function relationships, Proteins containing chemically modified amino acids: (natural proteins containing unnatural amino acids), Post-genomic biocatalysis: identification of the enzyme active sites and prediction of catalytic properties from gene sequences, Multi-array analysis. New protein and DNA biochip technologies, Non-invasive monitoring of blood chemistry, 'In silico' modeling of a cell: construction of "living" cells in computer. Biokinetic computer models for studies of gene expression and metabolism. IUPAC Organic and Biomolecular Chemistry Division (III) and Chemistry and Human Health Division (VII) project Number: 2001-005-1-300, last update March 2004 http://www.iupac.org/projects/2001/2001-005-1-300.html

Post genomic chemistry: the implication of advances in genomics, proteomics, biomimetics, and biological and chemical informatics. Such advances involve combinatorial chemistry and automated chemical synthesis, synthesis of new classes of unnatural amino acids, development of new biosynthesis methods for preparation of proteins containing unnatural amino acids, chemical management of biosystems at the molecular level, and self-multiplying polymers. Chemistry International Vol. 26 No. 2 March-April 2004 http://www.iupac.org/publications/ci/2004/2602/pp1_2001-005-1-300.html

privileged structures: Molecular scaffolds capable of interacting with a variety of cellular targets. The application of the privileged structure concept in the design of libraries can play a crucial role for the identification of high- affinity ligands. Privileged structures in drug design, France http://privilegedstructures-drugdisc.ifrance.com/Leading%20References.html 

Evans, BE et. al, Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists, Journal of  Medicinal Chemistry 31(12): 2235- 2246, Dec. 1988

process chemistry: Bioprocessing glossary

residue, scaffold, small molecule libraries: Combinatorial libraries & synthesis glossary

restriction endonucleases: Genetic manipulation & disruption glossary

reverse chemical genetics: A[nother] way to discover a useful chemical tool is to start with the desired protein target and screen for small molecules that affect its activity, then ask whether the small molecule causes a phenotypic change in an organism or cell. This approach is analogous to reverse genetics, in which a gene is deliberately mutated or knocked out in order to study the resulting phenotype. Reverse chemical genetics has been extensively used in the pharmaceutical industry and has in some cases led to surprising advances in biological understanding. Biology Overview Initiative for Chemical Genetics, Institute of Chemistry and Cell Biology, Harvard Medical School, US  http://iccb.med.harvard.edu/biology/ 

reverse chemical proteomics: The proteome is expressed on the surface of an amplifiable vector and then probed with a tagged small molecule. The only example currently available is display cloning, using phage display of a cDNA library (transcriptome) and panning this library with a small molecule probe (drug or natural product). Andrew M. Piggott and Peter Karuso, Quality Not Quantity: The Role of Natural Products and Chemical Proteomics in Modern Drug Discovery, Combinatorial Chemistry and High Throughput Screening, 7(7): 607- 630. 2004

Related terms: forward chemical genetics;  Genetic manipulation & disruption glossary reverse genetics, reverse genomics

scaffold hopping:  the definition of scaffold hopping and, more importantly, the detection of what constitutes a scaffold hop, is also ill-defined and highly subjective. Essentially, it is agreed that scaffolds should be substantially different from each other, although significantly similar to each other, to constitute a hop. In the latter, the scaffolds must permit a similar geometric arrangement of functional groups to permit the mode of action. However, this leaves the paradox of how to describe both scaffold similarity and dissimilarity simultaneously. In this paper, the current statuses of scaffolds and scaffold hopping are reviewed based on published examples of scaffold hopping from the literature. An investigation of the degree to which it is possible to formulate a more rigorous definition of scaffolds and hopping in the context of molecular topologies is considered. N Brown, E Jacoby, On scaffolds and hopping in medicinal chemistry. Mini Rev Med Chem 6 (11) :1217- 1229, Nov 2006  Related term: molecular scaffold.

A primary goal of 3D similarity searching is to find compounds with similar bioactivity to a reference ligand but with different chemotypes, i.e., "scaffold hopping". However, an adequate description of chemical structures in 3D conformational space is difficult due to the high- dimensionality of the problem. We present an automated method that simplifies flexible 3D chemical descriptions in which clustering techniques traditionally used in data mining are exploited to create "fuzzy" molecular representations called FEPOPS (feature point pharmacophores). A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes, JL Jenkins, M Glick, JW Davies Journal of Medicinal Chemistry 47 (25): 6144- 6159, Dec. 2, 2004

Related term?: molecular scaffold,  target hopping

selectivity: See analytical specificity Genetic & genomic testing glossary

sensitivity (in analytical chemistry): Genetic & genomic testing glossary

solubility: A basic phenomenon underlying most industrial processes. The objective of this project is to prepare a book that will bring together recent developments in solubility studies … especially that rigorous work which is underpinned by thermodynamic considerations. … will include chapters on super critical fluids, data banks, "green chemicals", molten salts, liquid-liquid phase equilibria, nanotechnology, industrial solutions including cryogenic solutions, predictions, simulations and molecular modeling, gases in polymers, metallurgical and hydrometallurgical processes, food, pharmaceutical and cosmetics industry and separation processes. Developments and applications in solubility, Physical and Biophysical Chemistry Division (I) and Analytical Chemistry Division (V) IUPAC project Number: 2005-016-1-100, last update July 2005 http://www.iupac.org/projects/2005/2005-016-1-100.html

specialty chemicals: See under fine chemicals

structural chemogenomics As structure determination provides an increasingly complete three dimensional and functional view of genomic biology, various approaches will be utilized to identify selective small molecule ligands for proteins on a genomic scale.  This will be defined as "structural chemogenomics" and will undoubtedly provide new opportunities for drug development as new synthetic chemistries develop, computational tools advance, and protein families are understood at the atomic level. [Sara Dry et. al "Structural genomics in the biotechnology sector"  Nature Structural Biology supplement 7:946 - 949, Nov. 2000]  

target hopping: Drug targets glossary

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IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms in Quantities and Units in Clinical Chemistry, Biochim Clin 1995; 19: 471-502. Around 300 definitions  Pure & Applied Chemistry 68: 957- 1000, 1996 
IUPAC International Union of Pure and Applied Chemistry, Basic Terminology of Stereochemistry Recommendations, 1996. 250+ definitions. http://www.chem.qmw.ac.uk/iupac/stereo/
IUPAC International Union of Pure and Applied Chemistry, GLOSSARY FOR CHEMISTS OF TERMS USED IN TOXICOLOGY Clinical Chemistry Division, Commission on Toxicology, Recommendations. Pure and Appl. Chem., 65 ( 9):  2003-2122, 1993. 1200+ definitions.   http://sis.nlm.nih.gov/enviro/glossarymain.html   http://www.iupac.org/reports/1993/6509duffus/
IUPAC International Union of Pure and Applied Chemistry, Nomenclature in laboratory robotics and automation, 1994 http://www.iupac.org/publications/pac/1994/pdf/6603x0609.pdf
IUPAC, Glossary of terms used in theoretical organic chemistry, 1999 http://www.iupac.org/publications/pac/1999/71_10_pdf/7110mirkin_1919.pdf
Oxford Dictionary of Biochemistry and Molecular Biology, Oxford University Press, Over 17,000 main entries. To order: http://www.oup.co.uk/isbn/0-19-850673-2

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IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.