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Medicinal & Pharmaceutical Chemistry glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS
Last revised January 09, 2020

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. 

Related glossaries include  Assays & screening  Bioprocessing    Combinatorial libraries & synthesis    Drug discovery & development    Drug targets   Metabolic engineering    Pharmacogenomics  
Informatics: Cheminformatics  Drug discovery informatics 
Technologies:   Labels, signaling & detection
   Mass spectrometry    Microarrays   Miniaturization & nanoscience  
Biology: Expression gene & protein  Nomenclature  Pharmaceutical biology

aliquot in analytical chemistry: A known amount of a homogeneous material, assumed to be taken with negligible sampling error. The term is usually applied to fluids. The term 'aliquot' is usually used when the fractional part is an exact divisor of the whole; the term 'aliquant' has been used when the fractional part is not an exact divisor of the whole (e.g. a 15 ml portion is an aliquant of 100ml). When a laboratory sample or test sample is 'aliquoted' or otherwise subdivided, the portions have been called split samples. IUPAC Gold Book

Analytical Support for Drug Product Development May 4-8, 2020 Boston, MA  Overcoming the Analytical and Formulation Challenges of a New Generation of Drug Products  Advances in protein science, drug combinations, delivery technology and analytical methods are supporting an unprecedented wave in novelty in the design of biologic drug products. With these new products comes the urgent need for analytical support of product development, regulatory filings and manufacturing – in ways that require a constant adaptation by analytical and formulation groups to new modalities and technologies.

API active pharmaceutical ingredients  The dosage form for a pharmaceutical contains the active pharmaceutical ingredient (API), which is the drug itself, and excipients, which are the substances of the tablet, or the liquid the API is suspended in, or other material that is pharmaceutically inert. Drugs are chosen primarily for their active ingredients.  Wikipedia accessed 2018 Dec 2

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  Related terms: chemical genomics, chemogenomics

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: publishes research that addresses biological questions at the molecular level, using organic chemistry and principles of physical organic chemistry. The scope of the journal covers a range of topics at the organic chemistry-biology interface, including: enzyme catalysis, biotransformation and enzyme inhibition; nucleic acids chemistry; natural product chemistry and natural product biosynthesis; antimicrobial agents; lipid and peptide chemistry; biophysical chemistry; and biomimetic chemistry.  BioOrganic Chemistry, Elsevier Scope note

Biophysical Approaches for Drug Discovery New Methods and Lead Generation Strategies for Medicinal Chemists APRIL 12, 2019 San Diego CA Recent advances in automation and sensitivity of biophysical approaches for measuring biomolecules interacting with one another has spurred progress in drug discovery. Technologies such as nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), other biosensor-based assays, isothermal titration calorimetry (ITC), and thermal shift assays (TSAs) have enabled discovery of compounds targeting protein-protein interactions and complex membrane protein targets. These target classes are more difficult to ‘drug’ because they are either harder to solubilize or not as amenable as are traditional intracellular enzyme targets to in-vitro-based, biochemical functional assays for high throughput screening. Fragment-based drug design is also another lead generation approach that is very dependent on biophysical technologies.

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

Biotherapeutics Analytical Summit
Biotherapeutics Analytical Summit  June 1-5, 2020 • Alexandria VA | brings together analytical scientists from biotherapeutics discovery, analytical development, pharmaceutical sciences, process development, formulation, technical development to discuss experiences and share best practices on selecting, developing and characterizing new & emerging molecules and bringing them faster to clinic, and to market.

biotransformation: The chemical conversion of substances by living organisms or enzyme preparations. IUPAC Medicinal Chemistry

The chemical alteration of an exogenous substance by or in a biological system. The alteration may inactivate the compound or it may result in the production of an active metabolite of an inactive parent compound. The alteration may be either non- synthetic (OXIDATION- REDUCTION; HYDROLYSIS) or synthetic (glucuronide formation, sulfate conjugation, ACETYLATION; METHYLATION). This also includes metabolic detoxication and clearance. MeSH, 1970

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

Characterization of Biotherapeutics  January 20-21, 2020 San Diego, CA |  leading scientists from biopharmaceutical industry, academia and government will discuss case studies, new technologies, assays on analytical development and characterization of mAbs, ADCs, bispecifics, and other novel protein formats, biosimilar. Some of the hot topics for discussion this year will include discuss regulatory expectations and developability of new product formats, cell and gene therapy products, biosimilars, high-throughput analytics, multi-attribute methods, glycosylation/post-translational modifications and biophysical assays

Characterization of Biotherapeutics  Exploring the Analytical Challenges of Today’s Complex Biologics May 4-5 2020   Boston MA As new product formats progress through development and into the regulatory process, the role of analytical characterization is taking on new meaning. Very new modalities present challenges to both analytical scientists and regulatory agencies alike, and this steep learning curve requires a near-constant cycle of adaptation and innovation. The agencies are requiring sponsors to provide ever more complex data across a wide range of analytical methods, and instrumentation suppliers are striving to support this new era with unique product features, software and feature combinations.

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  Related term: chemical genomics

chemical genetics: "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   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 mutagenesis:  Systematic mutagenesis using chemical with mutagenic properties.

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.

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 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

chemical tools:  small molecules used as probes of a chemical or biological process. Studying the effects of chemical tools on a system can lead to new insight into the molecular target of the small molecule and the pathways it acts in. Chemical probes with defined targets can be attractive as drugs in clinical pharmacology.
Related term: tool compounds

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

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). ;;; chemogenomics or chemical genomics, is the systematic screening of targeted chemical libraries of small molecules against individual drug target families (e.g., GPCRsnuclear receptorskinasesproteases, etc.) with the ultimate goal of identification of novel drugs and drug targets.[1] Typically some members of a target library have been well characterized where both the function has been determined and compounds that modulate the function of those targets (ligands in the case of receptorsinhibitors of enzymes, or blockers of ion channels) have been identified. Other members of the target family may have unknown function with no known ligands and hence are classified as orphan receptors. By identifying screening hits that modulate the activity of the less well characterized members of the target family, the function of these novel targets can be elucidated. Furthermore, the hits for these targets can be used as a starting point for drug discovery. The completion of the human genome project has provided an abundance of potential targets for therapeutic intervention. Chemogenomics strives to study the intersection of all possible drugs on all of these potential targets.[2] Wikipedia accessed 2018 Aug 22

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

Chemistry Manufacturing & Controls CMC: To appropriately manufacture a pharmaceutical or biologic specific manufacturing processes, product characteristics, and product testing must be defined in order to ensure that the product is safe, effective and consistent between batches.  These activities are known as CMC, chemistry, manufacturing and control. All stages of the drug development life cycle, after drug discovery involve CMC.  During preclinical drug development, the proper analytical methods are validated to monitor the product.  Stability testing may be initiated, the physicochemical properties of the product are determined, raw materials are chosen and tested.  When the drug development process moves into the clinical stage, further analytical method validation is required, and additional characterization of the drug product is needed.  After clinical trials the scale up process must ensure that the larger batches of product are the same and meet the same specifications as the drug tested in the clinical trials.  After the manufacturing process is qualified, lot release and in process testing will continue to take place. Pacific BioLabs
FDA Pharmaceutical Quality CMC guidelines 
See also Bioprocessing,   Drug Discovery & Development

chemoproteomics:  The use of biological information to guide chemistry--offers a highly efficient alternative to small-molecule characterization that can accelerate drug discovery. Beroza P, Villar HO, Wick MM, Martin GR. Chemoproteomics as a basis for post-genomic drug discovery, Drug Discov Today, 7(15): 807- 814, Aug 1, 2002  Related terms: chemical proteomics, chemiproteomics

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 Photochem

compound: A chemical compound is a chemical substance composed of many identical molecules (or molecular entities) composed of atoms from more than one element held together by chemical bonds. A chemical element bonded to an identical chemical element is not a chemical compound since only one element, not two different elements, is involved. There are four types of compounds, depending on how the constituent atoms are held together: molecules held together by covalent bonds, ionic compounds held together by ionic bonds, intermetallic compounds held together by metallic bonds, certain complexes held together by coordinate covalent bonds.  Wikipedia accessed 2018 Dec 2

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   
Figures and tables 

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.   

compound validation: Assays & screening

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

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

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

Directed Evolution-Based Drug Discovery DNA Encoded Libraries and Other Diversity Oriented Platforms APRIL 9-10, 2019 San Diego CA Directed evolution approaches for drug discovery use genetic strategies (DNA-encoded, RNA-encoded or phage-based) to create very large but specific libraries of molecules whose amplification is driven by the target of interest. The theory was established decades ago but recently applications in early stage drug discovery have become more widespread. A few drug candidates arising from directed evolution campaigns are now in clinical trials. A bottleneck however of these diversity-oriented strategies is figuring out which hits to focus on from the many hits that are produced by these approaches.

Drug Discovery Chemistry  April 13-17, 2020 • San Diego, CA Program | Optimizing Small Molecules for Tomorrow's Therapeutics  Focused on discovery and optimization challenges of small molecule drug candidates,  including coverage of Artificial Intelligence for Early Drug Discovery

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 

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. Often, microreactors are used. Wikipedia accessed Oct 11 2017

forward [chemical] genetics:  Phenotypic screening of chemical libraries is used to identify drug targets (forward genetics) or to validate those targets in experimental models of disease (reverse genetics).[2    Wikipedia Chemical Genetics accessed 2018 July 23  

Fragment-Based Drug Discovery      

Fragment-Based Drug Discovery From Hits to Leads and Lessons Learned APRIL 14-15. 2020 Fragment-based drug discovery (FBDD) has proven to be a successful approach for finding new drug compounds, especially against difficult targets such as intracellular protein-protein interactions (PPIs). Quite a few drugs on the market today can trace their origins to hits from fragment-based library screening campaigns. Now that FBDD has been folded into many early drug discovery departments, questions such as how to merge hits arising from fragment-based screens with hits from traditional high throughput screening methods are more frequent. Plus, the challenge of growing fragment hits into drug leads still remains, especially when the fragment and target do not have co-crystal structures to guide ligand design

genochemistry genomic chemistry: The volume of data from biological and chemical studies has been increasing exponentially in recent years. In particular, there are now 150 billion sequences within GenBank, 60k protein structures in PDB, and 50 million chemicals with unique structures (as of  Sept. 7, 2009, CAS).  As a result, one of the most important challenges has been the annotation of genetic sequences to their functions, and enzymes (encoded by their sequences) to their substrate profiles.  A systematic study of chemistry that links the enzyme's sequence information (including SNP) and substrate structural diversity is needed.  It differs from traditional disciplines in many ways and requires a restructuring of established methods, the standardization of the data collection process, and new bioinformatics and modeling tools. It can take the form of extended biocatalysis complemented by bioinformatics and molecular modeling. We tentatively refer to this discipline as Genochemistry. IUPAC, Genochemistry -- chemistry designed for life sciences: Towards a guideline and a framework of genochemistry, 2010  IUPAC Project Number 2009-021-3-300.  A glossary of specialized terms will be included.

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

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

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.   

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: Study of biochemical and molecular aspects of immunology, especially the nature of antibodies, antigens and their interactions. IUPAC Gold Book

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. Completed 2014  

isomer: Molecules with identical molecular formulas but different structural formulas. Fred Senese, General Chemistry Glossary, Frostburg State University, 2001]

lipophilicity: represents the affinity of a molecule or a moiety  for a lipophilic  environment. It is commonly measured by its distribution behaviour in a biphasic system, either liquid-liquid (e.g., partition coefficient  in 1-octanol/water) or solid-liquid (retention on reversed-phase high-performance liquid chromatography  (RP-HPLC) or  thin-layer chromatography   (TLC) system). IUPAC Gold Book

kDA: Kilo Dalton

Kinase Inhibitor Chemistry
Kinase Inhibitor Chemistry April 14-15, 2020 • San Diego, CA | Kinase inhibitor discovery is a very active area as developers are exploring more deeply into designing immune-modulatory agents as single or combination therapies, tackling chronic disease indications, such as inflammation and CNS disorders, as well as effectively harnessing allosteric modulators, and covalently binding compounds. will also be discussing the role of artificial intelligence, new and non-oncology drug targets, phosphatases, and protein degraders in kinase development.

Macrocyclics and Constrained Peptides
Macrocyclics and Constrained Peptides
 April 14-15, 2020 • San Diego, CA | In the drug discovery industry, synthetic macrocyclic compounds theoretically fit the bill for new chemical entities that have good drug potential yet can access newer drug targets such as protein-protein interactions (PPIs) that are intracellular and more complex than traditional enzymatic targets. Indeed, there are examples of naturally occurring macrocyclics, such as cyclosporin, that have become successful drug compounds. Synthetic macrocyclics' 'idealness,' however, is still being optimized.

materials chemistry: comprises the application of chemistry to the design, synthesis, characterization, processing, understanding, and utilization of materials, particularly those with useful, or potentially useful, physical properties.

We propose the following working definition, based on a synthesis of the above suggestions and the currently accepted meaning of materials in most dictionaries and books:  Materials chemistry comprises the application of chemistry to the design, synthesis, characterization, processing, understanding, and utilization of materials, particularly those with useful, or potentially useful, physical properties.  This definition draws upon the existing definitions for the terms “chemistry” and “materials,” while acknowledging that the materials that have been (and are likely to continue to be) of particular interest to the practitioners are generally those that have certain properties—e.g., mechanical, electrical, magnetic, optical, etc.—that make them useful, or potentially useful, in a functional sense. Thus, the keywords “useful” and “properties” were added to further define the materials that are most likely to be the subject of investigation in this field as well as to acknowledge the fact that functionality, or the prospect of functionality, is a major driver for research and development in the field.  IUPAC  What Is "Materials Chemistry"? Vol. 31 No. 3  May-June 2009   Peter Day, Leonard Interrante, and Anthony West

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

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 


-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.

millamolecules: mid-range compounds that fall in size between small molecules and biologics. Size is not the only consideration for this class, as millamolecules should also be orally available and able to interrupt protein-protein interactions.   Bristol Myers Squibb: Areas of Focus

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 Barbalace "Molarity, Molality and Normality" 2006

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 Barbalace "Molarity, Molality and Normality" 2006 

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

natural products:    Related terms: Biomaterials  biomimetic materials, biomimetics

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
NIST, Organic Electronics

oxygen radicals: There are many types of radicals, but those of most concern in biological systems are derived from oxygen, and known collectively as reactive oxygen species. Oxygen has two unpaired electrons in separate orbitals in its outer shell. This electronic structure makes oxygen especially susceptible to radical formation… Biological Effects of Reactive Oxygen It is best not to think of oxygen radicals as "bad". They are generated in a number of reactions essential to life…  There is also a large body evidence indicating that oxygen radicals are involved in intercellular and intracellular signalling. … Despite their beneficial activities, reactive oxygen species clearly can be toxic to cells. By definition, radicals possess an unpaired electron, which makes them highly reactive and thereby able to damage all macromolecules, including lipids, proteins and nucleic acids.  R. Bowen, Colorado State University, Pathophysiology, Free radicals and reactive oxygen

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

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 

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

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 

privileged structures: Privileged structures are defined as molecular frameworks which are able of providing useful ligands for more than one type of receptor or enzyme target by judicious structural modification. Privileged structures: a useful concept for the rational design of new lead drug candidates. Duarte CD1Barreiro EJFraga CA. Mini Rev Med Chem. 2007 Nov;7(11):1108-19.

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. 

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

reagents: In the field of biology, the biotechnology revolution in the 1980s grew from the development of reagents that could be used to identify and manipulate the chemical matter in and on cells.[2][3] These reagents included antibodies (polyclonal and monoclonal), oligomers, all sorts of organisms and immortalised cell lines, reagents and methods for molecular cloning and DNA replication, and many others.[3][4] Tool compounds are also important reagents in biology; they are small molecules or biochemicals like siRNA or antibodies that are known to affect a given biomolecule—for example a drug target—but are unlikely to be useful as drugs themselves, and are often starting points in the drug discovery process.[5][6] Many natural products, such as curcumin, are hits in almost any assay in which they are tested, are not useful tool compounds, and are classified by medicinal chemists as "pan-assay interference compounds".[7][8][9]    Wikipedia accessed 2018 Nov 10

reverse [chemical] genetics: See under forward [chemical] genetics

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; 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 terms?: molecular scaffold,   Assays lead hopping,  target hopping

small molecules: Drug discovery & developmentsmall 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]  

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

tool compounds: Tool compounds usually constitute drug candidates with limited potential, either due to limited IP protection or limited application in humans. Despite their reduced potential as final drug candidate they represent a valuable tool for early drug discovery, early target validation and proof-of-concept studies. We are currently using such tool compounds to investigate the druggability and target validation of developmental transcription factors in the treatment of solid tumours, and intra cellular and membrane-bound receptors for the modulation of inflammatory responses.  Cooper Group, University of Queensland, Australia

Small molecular weight compounds of known structure from the literature that are not commercially available.  Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Chapel Hill   Related term: chemical tools

Chemistry resources
Chemistry Conferences
Drug Discovery Chemistry Chemistry Glossary, about 200 terms
IUPAC Compendium of Chemical Terminology Gold Book
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions.
IUPAC International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions.
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.
IUPAC Inernational Union of Pure and Applied Chemistry, Glossary of terms used in Computational Drug Design Part II, 2015
IUPAC International Union of Pure and Applied Chemistry, Glossary of terms used in Medicinal Chemistry, Part 1, 1998
IUPAC International Union of Pure and Applied Chemistry, Glossary of terms used in Medicinal Chemistry. Part II (IUPAC Recommendations 2013 
IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms used in Photochemistry, 3rd ed. 2006  
IUPAC International Union of Pure and Applied Chemistry, Glossary of Terms used in Physical Organic Chemistry, Recommendations 1994. 700+ definitions. Part of OneLook.
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
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.
IUPAC International Union of Pure and Applied Chemistry, Nomenclature in laboratory robotics and automation, 1994
IUPAC International Union of Pure and Applied Chemistry, Postgenomic Chemistry  Pure and Applied Chemistry 77 (9) , 1641 - 1654, 2005
IUPAC, Glossary of terms used in theoretical organic chemistry, 1999
Oxford Dictionary of Biochemistry and Molecular Biology, Oxford University Press,
Royal Society of Chemistry, RSC ontologies  Name Reaction Ontology RXNO, Chemical Methods Ontology CMO, Molecular Processes Ontology MOP 

How to look for other unfamiliar  terms

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

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