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Medicinal & Pharmaceutical Chemistry glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty 
mchitty@healthtech.com
Last revised October 10, 2014

 

 

Chemistry term index:  Finding guide to terms in these glossaries  Site Map  Related glossaries include  Drug discovery & development   Drug targets   Metabolic engineering  Pharmacogenomics  Informatics: Cheminformatics  Drug discovery informatics  Technologies: Assays & screening  Combinatorial libraries & synthesis   Labels, signaling & detection  Mass spectrometry  Microarrays   Miniaturization & nanoscience   Biology: Expression gene & protein  Nomenclature  Pharmaceutical biology

Chemistry comes into play in the form of chemical probes or as compounds being evaluated as potential leads or drugs. The use of chemical probes to elucidate biology is the basis of chemical genomics. A large series of compounds are individually introduced into cells, with the aim of identifying a cell that then undergoes a specific phenotypic change. By identifying the compound introduced into that cell, and then finding which gene or protein was bound by the chemical probe, the researcher succeeds in finding both a genetic link to a change in phenotype and a chemical probe that can cause that change to occur. 

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backup compounds:  Only about 20% of compounds that advance to clinical trials reach the market. Given this high rate of attrition and ever-increasing costs, companies need fallback plans as an alternative to canceling projects and writing off significant investments. Planning optimal backup compound strategies is often difficult. Back-Up Compound Strategies April 2012 Table of Contents | Tables and Figures 

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.sciencemag.org/content/286/5442/1153.abstract  Related terms: chemical genomics, chemogenomics

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

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

biophysical characterization: Technologies for include circular dichroism and Fourier-transform infrared spectroscopy

characterization: Can include determining identity, physical chemistry data,  purity, potency, quality, stability, strength, pharmacokinetics, dose response, and efficacy

I am still trying to understand all the nuances of "characterize" and "characterization" of genes, genomes, proteins and proteomes and how these relate to annotation and would welcome any insights from people working in these areas. Related terms: specified biotechnology product, well characterized; characterization, protein Proteins; Bioinformatics annotation Narrower term: biophysical characterization

chemical biology:  ACS Chemical Biology  provides an international forum for the rapid communication of research that broadly embraces the interface between chemistry and biology. The journal also serves as a forum to facilitate the communication between biologists and chemists that will translate into new research opportunities and discoveries. Results will be published in which molecular reasoning has been used to probe questions through in vitro investigations, cell biological methods, or organismic studies. We welcome mechanistic studies on proteins, nucleic acids, sugars, lipids, and nonbiological polymers. The journal serves a large scientific community, exploring cellular function from both chemical and biological perspectives. American Chemical Society, About the Journal  Chemical Biology http://pubs.acs.org/page/acbcct/about.html  Related term: chemical genomics

chemical biomarkers: Biomarkers
chemical cytometry: Ultrasensitivity

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

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

chemical ligand studies: Drug & disease targets
chemical markup language CML: Cheminformatics
chemical microarrays: Microarrays categories

chemical probes: The Molecular Libraries Program offers public sector biomedical researchers access to the large-scale screening capacity necessary to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. NIH Common Fund, Molecular Libraries https://commonfund.nih.gov/Molecularlibraries/overview.aspx

chemical proteomics:  The medical and pharmaceutical communities are facing a dire need for new druggable targets, while, paradoxically, the targets of some drugs that are in clinical use or development remain elusive. Many compounds have been found to be more promiscuous than originally anticipated, which can potentially lead to side effects, but which may also open up additional medical uses. As we move toward systems biology and personalized medicine, comprehensively determining small molecule-target interaction profiles and mapping these on signaling and metabolic pathways will become increasingly necessary. Chemical proteomics is a powerful mass spectrometry-based affinity chromatography approach for identifying proteome-wide small molecule-protein interactions. Nat Chem Biol. 2009 Sep;5(9):616-24. doi: 10.1038/nchembio.216. Target profiling of small molecules by chemical proteomics. Rix USuperti-Furga G.  http://www.ncbi.nlm.nih.gov/pubmed/19690537

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

Related term/equivalent?: chemiproteomics  

chemical self-assembly: Biomaterials

chemical shift: NMR & x-ray crystallography

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

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 http://www.nature.com/nrg/journal/v5/n4/box/nrg1317_BX1.html 

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  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

chiral: Having the property of chirality. As applied to a molecule the term has been used differently by different workers. Some apply it exclusively to the whole molecule, whereas others apply it to parts of a molecule. [IUPAC Compendium]

chirality: The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non- superimposable on its mirror image; such an object has no symmetry elements of the second kind. [IUPAC Compendium]  Related terms: enantiomer, handedness.

chromophore: That part of a molecular entity consisting of an atom or group of atoms in which the electronic transition responsible for a given spectral band is approximately located. IUPAC Bioinorganic IUPAC Photo 

compound
quality: Physicochemical properties such as lipophilicity and molecular mass are known to have an important influence on the absorption, distribution, metabolism, excretion and toxicity (ADMET) profile of small-molecule drug candidates. To assess the use of this knowledge in reducing the likelihood of compound related attrition, the molecular properties of compounds acting at specific drug targets described in patents from leading pharmaceutical companies during the 2000-2010 period were analysed. ...  we conclude that a substantial sector of the pharmaceutical industry has not modified its drug design practices and is still producing compounds with suboptimal physicochemical profiles. Paul D. Leeson and Stephen A St-Gallay The influence of the "organizational factor" on compound quality in drug discovery, Nature Reviews Drug Discovery, 10:749-765, October 2011 http://www.ncbi.nlm.nih.gov/pubmed/21959288   
Figures and tables http://www.nature.com/nrd/journal/v10/n10/fig_tab/nrd3552_ft.html 

congener: A substance literally con- (with) generated or synthesized by essentially the same synthetic chemical reactions and the same procedures. Analogs are substances that are analogous in some respect to the prototype agent in chemical structure.

Clearly congeners may be analogs or vice versa but not necessarily. The term congener, while most often a synonym for homologue, has become somewhat more diffuse in meaning so that the terms congener and analog are frequently used interchangeably in the literature. [IUPAC Medicinal Chemistry]

conformers: Molecules with the same molecular structure (same number of atoms and same atoms are bonded within the molecule) but with a different 3-Dimension representation due to twisting of various internal bonds   [United Devices Cancer Project FAQs http://members.ud.com/projects/cancer/faq_chem.htm   Compare: de novo structure

Dalton: Unit of mass equal to the unified atomic mass (atomic mass  constant). [IUPAC Compendium] After John Dalton (1766-1844) British chemist and physicist.

Frequently used in biochemistry to express molecular mass, although the name and the symbol [Da] have not been approved by CIPM [Comité international des poids et mesures] or ISO [International Organization for Standardization]. [IUPAC Quantities] 

de novo structure: A de novo structure, or de novo derivative, is a molecule that has actually been altered slightly rather than just contorted. [United Devices Cancer Project FAQs ]http://members.ud.com/projects/cancer/faq_chem.htm    Compare: conformer

dimer: A molecule which consists of two similar (but not necessarily identical) subunits. The term could also be used as a verb referring to the  act of the two subunits coming together (to dimerize). 09 Oct 1997  [OMD]

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

enantiomer: One of a pair of molecular entities that are mirror images of each other and non- superimposable. [IUPAC Bioinorganic] Also called optical isomers. Related terms: chirality, racemate.

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 

flow chemistry: In flow chemistry a chemical reaction is run in a continuously flowing stream rather than in batch production. In other words, pumps move fluid into a tube, and where tubes join one another, the fluids contact one another. If these fluids are reactive, a reaction takes place. Flow chemistry is a well-established technique for use at a large scale when manufacturing large quantities of a given material. However, the term has only been coined recently for its application on a laboratory scale.  Wikipedia accessed Nov 1 2013 http://en.wikipedia.org/wiki/Flow_chemistry

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 forward genetics, forward genomics

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

handedness: Chirality and handedness are concepts that apply to the structure of molecules. Chirality is defined by the lack of certain features of symmetry, which lead to an object not being superimposable on its mirror image. Handedness is a different phenomenon relating to the ability to classify chiral objects into right-handed and left-handed objects. All handed objects are chiral, but not all chiral objects are handed. In 1968 through 1970, Ruch and coworkers developed a theory of chirality that provided a mathematical basis for the handedness of chiral objects. Handed chiral objects are considered to be analogous to shoes, which are readily classified into right and left shoes regardless of the size, material, style, or other attributes of the shoes in question. Nonhanded chiral objects are considered to be analogous to potatoes, which have no symmetry because of their irregular patterns of "bumps" and "eyes," thereby meeting the lack of symmetry requirements for chirality. There is, however, no unambiguous way to classify a set of potatoes into "left" and "right" potatoes. RB King, Chirality and handedness: the Ruch "shoe-potato" dichotomy in the right- left classification problem, Annals of the  New York Academy of Sciences 988: 158- 170, May 2003 Related term: chirality

hapten: A molecule (usually a small organic molecule) which can be bound to an antigenic determinant/ epitope. Usually they are too small to give a response of their own. They become antigenic if they are coupled to a suitable macromolecule, such as a protein. IUPAC Bioinorganic

Small antigenic determinants capable of eliciting an immune response only when coupled to a carrier. Haptens bind to antibodies but by themselves cannot elicit an antibody response. MeSH, 1965

hard drug: A nonmetabolizable compound, characterized either by high lipid solubility and accumulation in adipose tissues and organelles, or by high water solubility.   In the lay press the term "hard Drug" refers to a powerful drug of abuse such as cocaine or heroin.  IUPAC Medicinal Chemistry

heterodimer: biochemistry A dimer in which the two subunits are different.   

high content analysis: Assays & Screening

hydrophilicity: The tendency of a molecule to be solvated by water. IUPAC Medicinal Chemistry  

hydrophilization: The process of modifying proteins or polymers to make them more stable. A number of methods can be used. 

hydrophobicity is the association of non-polar groups or molecules in an aqueous environment which arises from the tendency of water to exclude non polar molecules. (See also Lipophilicity). IUPAC Medicinal Chem

immunochemistry: The field of immunochemistry is becoming increasingly important in different disease states with respect to the development of diagnostics and therapeutics. The objective is to compile present knowledge of the molecular basis of immunochemical interactions, to summarize the rapidly expanding applications in many health-related areas, and to critically discuss the upcoming research needs…. These projects are of importance especially to occupational and environmental health. The present project will add important new aspects to IUPACs involvement in immunochemistry by describing advances in the understanding of chemical interactions between antigens and T-cell receptors (TCR) or immunoglobulins, and depicting how immunochemical applications presently improve and diversify medical diagnostics and therapeutics. IUPAC Advances in immunochemistry and applications to human health Project No.:2010-050-1-700http://www.iupac.org/nc/home/projects/project-db/project-details.html?tx_wfqbe_pi1%5bproject_nr%5d=2010-051-1-700

isomer: Molecules with identical molecular formulas but different structural formulas*. [Fred Senese, General Chemistry Glossary, Frostburg State University, 2001] http://antoine.frostburg.edu/chem/senese/101/glossary.shtml

kDA: Kilo Dalton

Macrocycles: Discovery, Development & Technologies 2013 Table of Contents | Tables and Figures

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: Mastering Medicinal Chemistry May 21-22, 2014 • Boston, MA Program | Register | This year’s event will include discussions around the future role of medicinal chemistry and explore how it will contribute to improved drug discovery success rates. Senior level chemists from across the industry will discuss how kinetics and residence time, targeted tissue delivery, and allosteric inhibitors will enhance profiles or modulate difficult targets.

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

It has been 10 years since the first [IUPAC] Glossary of Terms Used in Medicinal Chemistry was published. During this period, a remarkable change in medicinal chemistry practice has occurred, largely in response to the genomic revolution, including the introduction of combinatorial chemistry, robotic techniques, and parallel synthesis. It has brought with it an accompanying vocabulary of new terminology. There is a particular need to address the terminology associated with chemogenomics, chemoinformatics, newer strategies for hit and lead discovery, and those parameters that deal specifically with chemical diversity and drug-likeness.  Chemistry International Mar-Apr 2009 http://www.iupac.org/publications/ci/2009/3102/pp2_2008-010-1-700.html 

A thorough analysis of recent trends in medicinal chemistry and evaluation of their significance for advancing productivity in drug discovery is presented. This report includes a critical evaluation of chemical and computational technological modalities, their current and potential value, and their commercial manifestations, a consideration of market dynamics with an emphasis on outsourcing and user views on the implications of current practices in drug discovery organizations and insights gleaned from an extensive literature review, discussions with industry experts, and an opinion survey of personnel active in medicinal chemistry for drug discovery. Insight Pharma Reports, Medicinal Chemistry for drug discovery: Significance of recent trends, 2009
Narrower term: dynamic medicinal chemistry

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   

-mer: This suffix is often used to indicate the number of nucleotides in an oligonucleotide, e.g. 30-mer, 19-mer. [ICN]  Related terms dimer, monomer, trimer, up to 10 nucleotides decamer.  Eleven and above are the number plus -mer.

microchemical systems, microchemistry: Miniaturization & nanoscience

molality: The molal unit is not used nearly as frequently as the molar unit. A molality is the number of moles of solute dissolved in one kilogram of solvent. Be careful not to confuse molality and molarity. Molality is represented by a small "m," whereas molarity is represented by an upper case "M."  [Roberta Crowell Barbarlace "Molarity, Molality and Normality" Environmental Chemistry.com, 1995-2001] http://environmentalchemistry.com/yogi/chemistry/MolarityMolalityNormality.html

molarity: The molar unit is probably the most commonly used chemical unit of measurement. Molarity is the number of moles of a solute dissolved in a liter of solvent. [Roberta Crowell Barbarlace "Molarity, Molality and Normality" Environmental Chemistry.com, 1995- 2001] http://environmentalchemistry.com/yogi/chemistry/MolarityMolalityNormality.html

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: Regulatory

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  biomimetic materials, biomimetics

nanochemistry: Miniaturization & nanoscience

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 

PAINS Pan Assay Interference Compounds: A true drug inhibits or activates a protein by fitting into a binding site on the protein.  Artefacts have subversive reactivity that masquerades as drug-like binding and yields false signals across a variety of assays.  These molecules. have defined structures, covering several classes of compounds. … But biologists and inexperienced chemists rarely recognize them. .. Time and research money are consequently wasted in attempts to optimize the activity of these compounds. Chemical con artists foil drug discovery, Jonathan Baell, Michael A. Walters, Nature  513: 481-483,  25 Sept 2014 doi: 10.1038/513481a   http://www.ncbi.nlm.nih.gov/pubmed/25254460

peptides: Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. IUPAC http://goldbook.iupac.org/P04479.html 

Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES. MeSH

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 Related terms: -Omes & -omics  peptidome, peptidomics Wikipedia http://en.wikipedia.org/wiki/Peptidomimetic 

peptidomics: -Omes & -omics
performance chemicals: See under fine chemicals
pharmacophore: Drug & disease targets 
photochemistry: Molecular imaging

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

privileged structures: The concept of so-called "privileged structures" was initially proposed by scientists at Merck in 1980s (see ref. Journal of Medicinal Chemistry, 31, 2235-2246, 1988). They observed in their research at Merck that certain type of structures were preferred by certain class of receptors (proteins). ... It appears that the main function of the privileged structure in a drug molecule is to position those functional groups that are attached to it in a right direction and help them interact with the receptor properly. Therefore, it's logical to think that by replacing the privileged structure of a drug molecule while keeping those functional groups unchanged, we might find a better drug.  Shanghai Syncores Technologies Inc http://www.syncores.net/priviledged.htm 

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   

protein chemistry:
The Protein Chemistry Department provides and supports the protein purification and characterization needs of Research. This includes both large-scale reagent and micropurifications. The department is largely responsible for the maintenance of the protein request system, a web based system that allows researchers to request protein purifications. The department also strives to maintain and build our technology edge. These areas include refolding of proteins, protein conjugations (especially drug-antibody conjugations), protein sequencing and mass spectrometry. The department also provides protein chemistry support for TAP, TAHO and Angiogenesis project teams.  Genentech, Protein Chemistry, Science of Biotechnology http://www.gene.com/gene/research/biotechnology/proteinchemistry.html 

racemate: An equimolar mixture of a pair of enantiomers. It does not exhibit optical activity. The chemical name or formula of a racemate is distinguished from those of the enantiomers by the prefix (±)- or rac- (or racem-) or by the symbols RS and SR. [IUPAC Compendium]  Related term: enantiomer

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 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 Molecular diagnostics

sensitivity (in analytical chemistry): Molecular diagnostics

small molecules: Drug discovery & development; small molecule libraries

solubility: SOLUBILITY is one of the most basic and important of thermodynamic properties, and a property which underlies most industrial processes. This book is a collection of 24 chapters involving recent research works, all related to solubility. The objective is to bring together research from disparate disciplines which have a bearing on solubility. Links between these chapters, we believe, could lead to new ways of solving problems and looking at new and also old solubility related issues.  Developments and Applications in Solubility, Trevor M. Letcher (ed.) The Royal Society of Chemistry, 2006 [ISBN 0 85404 372 1; ISBN-13 978 0 85404 372 9]   http://old.iupac.org/publications/books/author/letcher07.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]  

systems chemical biology: The integration of chemistry, biology and computation to generate understanding about the way small molecules affect biological systems as a whole. Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research. David J. Wild,  Ying Ding,  Amit P. Sheth  ,  Lee Harland,  Eric M. Gifford, Michael S. Lajiness , Drug Discovery Today, January 2012 http://lists.w3.org/Archives/Public/public-semweb-lifesci/2012Jan/att-0020/Wild_2012_SystemsBioSW.pdf

target hopping: Drug targets

Bibliography
Chemistry Conferences http://www.chicorporate.com/Conferences/Search.aspx?k=&r=&s=CHM
Drug Discovery Chemistry http://www.drugdiscoverychemistry.com/
High Content Analysis http://www.highcontentanalysis.com/

Chemistry CDs, DVDs http://www.chicorporate.com/Conferences/CompactDiscs.aspx?s=CHM
Chemistry Short courses http://www.healthtech.com/Conferences_Upcoming_ShortCourses.aspx?s=CHM

Insight Pharma Reports Chemistry series
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about.com Chemistry Glossary, about 200 terms http://chemistry.about.com/library/glossary/blglossary.htm
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IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms Used in Combinatorial Chemistry, D. Maclean, J. J. Baldwin, V.T. Ivanov, Y. Kato, A. Shaw, P. Schneider, and E. M.. Gordon, Pure Appl. Chem., Vol. 71, No. 12, pp. 2349-2365, 1999. 100+ definitions. http://www.iupac.org/reports/1999/7112maclean/
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IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms used in Photochemistry, 3rd ed. 2006 http://iupac.org/publications/pac/79/3/0293/  
IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms used in Physical Organic Chemistry, Recommendations 1994. 700+ definitions. Part of OneLook. http://www.chem.qmw.ac.uk/iupac/gtpoc
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 International Union of Pure and Applied Chemistry, Postgenomic Chemistry  Pure and Applied Chemistry 77 (9) , 1641 - 1654, 2005 
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IUPAC, Glossary of terms used in theoretical organic chemistry, 1999 http://www.iupac.org/publications/pac/1999/71_10_pdf/7110mirkin_1919.pdf
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Royal Society of Chemistry, RSC ontologies  http://www.rsc.org/ontologies/  Name Reaction Ontology RXNO, Chemical Methods Ontology CMO, Molecular Processes Ontology MOP 

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