Created by: Caty Chung, Nicolette Ross, Joan Glenny-Pescov, Jiaming Hu, Stephan Schurer*
Contact: Stephan Schurer stephan dot schurer at med dot miami dot edu
An oxidative enzyme that catalyzes the conversion of luciferin to oxyluciferin with the concomitant emission of light (luminescence).
Lipids are a group of naturally occurring organic compounds that are soluble in nonpolar organic solvents, but insoluble in water. Examples include fatty acids, triglycerides, phospholipids, etc. Lipids function to store energy, form a component of cell membrane and as signaling molecules.
A protein or polypeptide is a long polymer of amino acids joined together by peptide bonds. The sequence of the amino acids is defined by the genetic code. Here, a protein is a perturbagen whereby its ability to modulate a physiological process or a disease pathology is assessed.
Includes all hydrolases except phosphatases and proteases.
PNA or protein nucleic acid is an artificially synthesized polymer whose backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. Since PNA does not contain charged phosphate groups in its backbone, the interaction between PNA-DNA is stronger than that between DNA-DNA due to the lack of electrostatic repulsion.
Viruses are small infectious agents that depend on the host cells to reproduce. Outside the host, they contain a protein coat called capsid that encloses their genetic material (either DNA or RNA). Viruses can infect bacteria, plants and animals and cause a number of diseases, e.g. smallpox, chickenpox, influenza, polio, rabies, etc.
It includes the baker's yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), which are unicellular.
The proteins located on the cell surface which are involved with the binding with other cells or the extracellular matrix. They belong to 5 families: Immunoglobulin superfamily, integrins, cadherins, selectins and the lymphocyte homing receptors.
Cells that are cultured from a subject (tissue or tumor) and which are not immortalized. They can undergo only a limited number of cell divisions prior to reaching senescence.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end (from GO).
DNA or deoxyribonucleic acid is the genetic material in all the living things, and some viruses. It is a polymer of nucleotides, with a backbone made of deoxyribose sugar and phosphate groups joined together by ester bonds.
RNA or ribonucleic acid is a polymer of nucleotides with a backbone made of ribose sugar and phosphate groups linked together by ester bonds. RNA has the base uracil instead of thymine, which is present in DNA.
mRNA or messenger RNA is a genetic intermediate between DNA and protein. It is transcribed from DNA by RNA polymerases which is further processed by other enzymes. mRNA serves as the template to synthesize proteins on the ribosomes.
rRNA or ribosomal RNAs are present in ribosomes in a cell. Ribosomes are protein translation machinery which can read messenger RNAs and translate that information into proteins.
tRNA or transfer RNA is a small RNA molecule that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis.
They have an essential role in the regulation of protein conformation states. Molecular chaperones help nascent polypeptides fold correctly and multimeric protein complexes assemble properly, and reduce the possibility of protein aggregation.
Enzymes are biological catalysts involved in important pathways that allow chemical reactions to occur at higher rates (velocities) than would be possible without the enzyme. Enzymes are generally globular proteins that have one or more substrate binding sites.
Ion channels are present in the cell membrane. They are pore-forming protein complexes that facilitate diffusion of ions across membranes and thus establish the small voltage gradient across the plasma membrane of living cells.
A membrane or intracellular protein that specifically binds a known stimulus of cellular activity, such as a hormone, growth factor, antigen, neurotransmitter, drug, etc.
It is a protein that binds to a specific sequence of DNA (upstream of the genes that it regulates) and regulates gene expression.
A transporter protein is a transmembrane protein that helps transport small molecules and proteins across the membrane. This is done using facilitated diffusion or active transport.
G protein-coupled receptors (GPCRs), comprise the largest integral membrane protein family with nearly 1000 members. They integrate extracellular signals from hormones, growth factors, neurotransmitters, etc to downstream cellular responses. They are important pharmacological targets, being associated with a number of diseases. Upon ligand binding extracellularly, the GPCR signals through a downstream heterotrimeric G protein complex, consisting of the α, β and γ subunits.
Transmembrane receptors are integral membrane proteins in either the cell- or organelle-membrane. They bind specific hormones, neurotransmitters, cytokines, growth factors, etc and initiate cell signaling, which results in changes in the cell function.
Nuclear receptors are localized in the cytosol and mediate the activity of hormones and certain vitamins. They are all transcription factors, which upon activation by ligand binding, translocate to the nucleus, bind specific DNA sequence and activate gene expression.
Formation of two products from a substrate by hydrolysis.
Intramolecule rearrangement, i.e. isomerization changes within a single molecule.
Join together two molecules by synthesis of new C-O, C-S, C-N or C-C bonds with simultaneous breakdown of ATP.
Non-hydrolytic addition or removal of groups from substrates. C-C, C-N, C-O or C-S bonds may be cleaved.
To catalyze oxidation/reduction reactions; transfer of H and O atoms or electrons from one substance to another.
Transfer of a functional group from one substance to another. The group may be methyl-, acyl-, amino- or phosphate group.
Includes all transferases except kinases.
A protein kinase is an enzyme that modifies other proteins by chemically adding phosphate groups to them. The substrate protein's activity, localization and overall function is modulated by the kinase reaction.
A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysis of phosphoric acid esters.
cDNA or complementary DNA is complementary in sequence to a particular messenger RNA (mRNA). It is synthesized from mRNA in a reverse transcription reaction by reverse transcriptase enzyme. cDNA can be cloned in a vector and introduced into cells to bring about the expression of that particular gene in those cells.
DNA that is linear and not circular. Examples of linear DNA include synthetic oligonucleotide, restriction endonuclease digestion product, polymerase chain reaction product, mechanically sheared genomic DNA, etc.
Plasmid is a double stranded circular DNA molecule that can replicate independently of the chromosomal DNA. It exists naturally in bacteria and some yeast. In genetic engineering, plasmids are exploited to clone and multiply a gene of interest. Several plasmid vectors are available commercially to introduce cloned DNA into different cell types.
Peptide is a short polymer of amino acids, which is generally <50 amino acids long.
This includes animal models typically used in drug discovery for toxicity or pharmacology studies, such as mouse, rat (mammals).
Bacteria lack membrane bound organelles and are surrounded by a rigid cell wall. Though they are unicellular, they function by aggregating into multicellular colonies.
Proteins localized in the cytosol, but do not belong to the transcription factor, transporter, structural, enzyme, enzyme regulator and nuclear receptor classes of proteins in the cytosol.
Membrane proteins are associated with the cell membrane. They can be classified into two broad categories
There are two distinct G protein families, namely the heterotrimeric G proteins (consisting of the α, β and γ subunits) downstream of the G protein coupled receptors (GPCRs) and the monomeric G proteins that belong to the Ras superfamily of GTPases. Upon ligand binding, the GPCR undergoes a conformational change, which allows it to act as a guanine nucleotide exchange factor (GEF) of an associated G protein. The GTP-bound G α subunit then signals by regulating the activity of adenylate cyclase, phospholipase, or Rho GEFs.
These proteins are translocated from the inside of the cell to the cell's exterior. Proteins targeted for secretion undergo glycosylation and other postranslational modifications in the endoplasmic reticulum and the golgi complex, and are enclosed in secretory vesicles. The fusion of vesicles to the cell membrane releases the secretory proteins to the exterior. Examples include growth factors, tumor necrosis factors, cytokines, etc.
These proteins constitute the largest class with respect to the total protein mass. They are fibrous proteins, e.g. keratin, actin, myosin, etc whose primary function is to provide scaffolding that maintains cell shape.
This class includes membrane proteins other than g-proteins, such as regulators of g-protein, GTPases, etc.
Locked nucleic acid (LNA) is a nucleic acid analogue containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking sugar conformation. LNA oligonucleotides have high affinity toward complementary single-stranded RNA and complementary single- or double-stranded DNA. This makes LNA suitable for sequence specific targeting of RNA in vitro or in vivo.
Fungi are either unicellular or multicellular and include yeasts, molds, mushrooms, etc. Several parasitic fungi exist, which infect animals and plants, e.g., Aspergillus flavus, Claviceps purpurea, Pneumocystis jirovecii, etc.
Aptamers are synthetic affinity probes. RNA aptamers are oligonucleotides that bind to a specific target molecule such as small molecules, proteins, nucleic acids and cells. They are created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches.
They are part of mRNA that regulate gene expression through ligand induced changes in mRNA secondary or tertiary structure. The ligand is generally a small metabolite which binds to the aptamer part of the riboswitch.
Antibody is a protein (immunoglobulin) produced by the immune system of an organism in response to exposure to a foreign molecule (antigen) and characterized by its specific binding to a site of that molecule (antigenic determinant or epitope). Antibodies are used extensively as tools to characterize proteins. Antibodies are either monoclonal or polyclonal.
Highly specific antibodies produced by the clones of a single hybrid cell, which is generated by the fusion of a B cell with a tumor cell. They recognize a unique epitope of an antigen.
Antibodies produced by immunizing a mammal such as a mouse, rabbit or goat with an antigen. They are a mixture of antibodies produced from different B cells raised against any of the different epitopes of that antigen.
This includes fungi, vertebrates and invertebrates. Eukaryotic cells have a well-defined nucleus and membrane enveloped organelles namely, mitochondria, endoplasmic reticulum, golgi apparatus, and lysosomes.
This includes animals having a vertebral column, and model organisms from this group include the zebrafish, mouse, rat, etc
These animals lack a vertebral column and many of which are used as model organisms in HTS screening including Drosophila, C.elegans, sea urchin, etc.
This includes vertebrate model organisms such as the Danio rerio (zebrafish), Xenopus laevis, etc which are tested generally to understand development.
A brief description of the recombinant DNA created by the insertion of a gene or siRNA encoding DNA of interest into a vector. It includes information on the type of vector, the type of promoter, the selectable markers, etc., which are all considered when sub-cloning a gene of interest. The construct is transfected into cells by various methods.
The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.
Most of the fungi are multicellular, e.g. molds, mushrooms, etc. They are made up of multicellular filaments known as hyphae. Several parasitic fungi exist, which infect animals and plants, e.g., Aspergillus flavus, Claviceps purpurea, Pneumocystis jirovecii, etc.
A genomic sequence, which is the unit of heredity of a living organism. It consists of regulatory regions and transcribed regions.
They are living organisms which derive their energy from photosynthesis, with the exception of parasitic plants. Plants include herbs, shrubs, trees, grasses, vines, etc.
Causes mild infections such as "strep throat" to severe diseases such as necrotizing fasciitis and streptococcal toxic shock syndrome.
A protease is an enzyme that hydrolyzes the peptide bonds in a protein or a peptide.
This includes all organisms which are made up of cells, e.g. bacteria, plants and animals.
Metazoa comprises of animals, which are multicellular eukaryotic organisms. This includes those having a vertebral column (e.g. fish, frog, snake, bird, human) and those that do not (e.g. worm, fly, star fish, etc).
Protozoans are single celled organisms, some of which are parasitic, e.g., Plasmodium falciparum, Leishmania mexicana, Trypanosoma brucei, etc which cause malaria, leishmaniasis, and sleeping sickness, respectively.
Ac-DEVD-CHO is an inhibitor of caspase-3/7 (DEVDase) activity.
Ac-Trp-Glu-His-Asp-CHO Very potent reversible inhibitor of caspase-1 (ICE) that contains the optimal tetrapeptide recognition motif for this enzyme. With a Ki of 56 pM, it displays the most potent reversible, peptide-based inhibitors described for any protease. For caspase-8 a Ki of 21.1 nM has been reported.
The drug aprotinin (Trasylol, Bayer), is the bovine version of the small protein basic pancreatic trypsin inhibitor, or BPTI, which inhibits trypsin and related proteolytic enzymes.
Boc-Leu-Gly-Arg-AMC is a selective fluorogenic substrate for Horseshoe Crab Clotting Enzyme
A fluorogenic FRET peptide with a substrate sequence that is optimized for calpain-1 and -2.
fluorescein-labeled formylmethionine-leucine-phenylalanine-lysine (fmlfk-fitc) substrate for the formylpeptide receptor (FPR) family of G-protein-coupled receptors
fMLFF peptide is used as a FPR-blocking peptide.
guanine nucleotide-binding protein G(o) subunit alpha isoform a-Alexa Fluor 488
GM-TriDAP (GlcNAc-MurNAc-L-Ala-D-Glu-mesoDAP), is a muropeptide found mostly in Gram-negative bacterial peptidoglycan.
substrate for M1-family alanyl aminopeptidase (M1AAP)
LDV peptide targeted against the alpha4beta integrin VLA-4
substrate for virus-encoded NS3 serine proteinase
The peptide sequence, PHCVPRDLSWLDLEANMCLP, named R18, was identified as an unphosphorylated peptide that binds to 14-3-3 proteins with high affinity (Kd=80 nM). It has been shown to bind to the same amphipathic groove on the surface of 14-3-3 as phosphorylated peptides. R18 can inhibit the formation of the 14-3-3-Raf-1 complex, reduce Raf-1 dependent transcriptional activity in cells and block the activation of ExoS by 14-3-3. It binds to all the 14-3-3 isoforms with equal affinities. This peptide is useful for competitive inhibition experiments.
modulators of 14-3-3 proteins The 14-3-3 proteins are the prototype for a novel class of protein modules that can recognize phosphoserine/threonine (pS/T)-containing motifs in a variety of signaling proteins. To date, 14-3-3 proteins have been reported to bind more than 200 client proteins. Through these interactions, 14-3-3 proteins play important roles in a wide range of vital regulatory processes, such as Bad-induced apoptosis, Raf-1-mediated cell proliferation, and Cdc25-regulated cell cycle progression.
Ubiquitin-AMC is a fluorogenic substrate for a wide range of deubiquitinating enzymes (DUBs), including ubiquitin C-terminal hydrolases (UCHs) and ubiquitin specific proteases (USPs). UBIQUITIN-7-AMIDO-4-METHYLCOUMARIN
For use in the detection and identification of deubiquitinylating enzymes
This random polymer is a Tyrosine kinase substrate.
Selective agonist for the formyl peptide receptors FPR1, FPR2 (EC50 = 75 pM) and FPR3 (EC50 = 3 nM), expressed on immune cells. Trp-Lys-Tyr-Met-Val-D-Med-NH2
This is a fluorescent kallikrein substrate, Abs/Em=353/442 nm.
The plasmid, phagemid or viral genome that is used to recombinantly clone the DNA molecule of interest to be introduced into a host cell (bacterial, eukaryotic), where it can independently replicate.
Two or more proteins interact to form a stable complex. Each of the members of this complex has a distinct role in mediating the overall function of the complex, which can be as a chaperone (DnaK, DnaJ and grpE), an enzyme (mitochondrial respiratory complexes), a signaling complex (G-proteins), etc. It can be viewed as a quaternary structure of the proteins.
The individual protein molecule of a protein complex. In the complex, it associates with other protein subunits which are either the same or different, e.g., hemoglobin, microtubule, etc.
A clone of BHK (Baby hamster kidney) cells.
Recognizes a phosphorylated epitope (S/T)P found in phosphoproteins such as MAP2, HSP70, cdc25, and DNA topoisomerase IIa, most of which are phosphorylated at the onset of mitosis. The number of phosphoproteins recognized by MPM-2 varies from species to species and with the cell type.
calcium-mediated signaling using intracellular calcium
The categorization of different functional or non-functional elements in DNA.
The DNA region that is involved in initiating and modulating transcription.
The region of a gene that codes for RNA.
A synthetic DNA element that is known to be regulated by a transcription factor/s, which is cloned upstream of a gene of interest.
The regulatory DNA from a non-native gene, e.g., the regulatory region from the actin gene being cloned upstream of the myosin gene in a DNA construct.
The regulatory DNA from a native gene, e.g., the regulatory region from the actin gene being cloned upstream of the actin gene in a DNA construct.
has associated disease some disease or is bearer of disease (relation in new RO) Disease import from DOID
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together (from Gene Ontology).
Microtubule-associated proteins 1A/1B light chain 3B
Nuclear factor NF-kappa-B p65 subunit Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3
A protein that has been modified with either a molecular or protein and can be used either as a method of pulling down, antibody binding, luminescense, or tracer
An aldehyde oxidoreductase expressed predominantly in the LIVER; LUNGS; and KIDNEY. It catalyzes the oxidation of a variety of organic aldehydes and N-heterocyclic compounds to CARBOXYLIC ACIDS, and also oxidizes quinoline and pyridine derivatives. The enzyme utilizes molybdenum cofactor and FAD as cofactors.
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Broad substrate specificity ATP-binding cassette transporter ABCG2
Broad substrate specificity ATP-binding cassette transporter ABCG2 is encoded by the human ABCG2 gene. This protein is involved in the transport of urate, heme, porphyrin and xenobiotics.
Bile salt export pumpis encoded by the human ABCB11 gene. This protein plays a role in bile salt secretion.
The protein-coding gene EST1 located on the chromosome XII.
Reverse transcriptase subunit of the telomerase holoenzyme; essential for telomerase core catalytic activity, involved in other aspects of telomerase assembly and function; mutations in human homolog are associated with aplastic anemia.
Cytochrome P450 1A2 is encoded by the human CYP1A2 gene. This protein is involved in the hydroxylation of fatty acids, steroids and xenobiotics.
Cytochrome P450 2B6 is encoded by the human CYP2B6 gene. This protein plays a role in the metabolism of steroids and pharmaceuticals.
Cytochrome P450 2C19 is encoded by the human CYP2C19 gene. This protein is involved in steroid, terpenoid and drug metabolism.
Cytochrome P450 2C8 is encoded by the human CYP2C8 gene. This protein is involved in the oxidation of steroids, fatty acids, and xenobiotics.
Cytochrome P450 2C9 is encoded by the human CYP2C9 gene. This protein is involved in the oxidation of fatty acids, steroids and xenobiotics.
Cytochrome P450 3A4 is encoded by the human CYP3A4 gene. This protein is involved in the oxidation of steroids, fatty acids and xenobiotics.
This protein is involved in steroid, terpenoid and drug metabolism.
Cytochrome P450 2D6 is encoded by the human CYP2D6 gene. This protein plays a role in flavoprotein metabolism.
Cytochrome P450 3A7 is encoded by the human CYP3A7 gene. This protein plays a role in the oxidation of steroids, fatty acids, and xenobiotics.
Epoxide hydrolase 1 is encoded by the human EPHX1 gene. This protein is involved in the hydrolysis of cyclic organic compounds.
Cytochrome P450 3A5 is encoded by the human CYP3A5 gene. This protein is involved in the oxidation of steroids, fatty acids, and xenobiotics.
Multidrug and toxin extrusion protein 1 is encoded by the human SLC47A1 gene. This protein plays a role in transport of cationic drugs across membranes.
Multidrug and toxin extrusion protein 2 is encoded by the human SLC47A2 gene. This protein is involved in both excretion of toxic electrolytes and secretion of cationic drugs.
A protein that is a translation product of the human ABCB1 gene.
ATP-binding cassette sub-family C member 2
A protein that is a translation product of the human ABCC2 gene.
ATP-binding cassette sub-family C member 3
A protein that is a translation product of the human ABCC3 gene.
A protein that is a translation product of the human SLC15A1 gene.
The protein-coding gene FMO3 (flavin containing monooxygenase 3).
Catalyzes the oxidative deamination of primary and some secondary amine such as neurotransmitters, with concomitant reduction of oxygen to hydrogen peroxide and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues.
Catalyzes the oxidative deamination of primary and some secondary amines such as neurotransmitters, and exogenous amines including the tertiary amine, neurotoxin MPTP, with concomitant reduction of oxygen to hydrogen peroxide and participates in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues.
A protein that is a translation product of the human SLC22A6 gene.
A protein that is a translation product of the human SLC22A7 gene.
A protein that is a translation product of the SLC22A8 gene.
Solute carrier organic anion transporter family member 1B1
Solute carrier organic anion transporter family member 1B1 is encoded by the human SLCO1B1 gene. This protein is involved in the sodium-independent uptake of endogenous compounds in the liver.
Solute carrier organic anion transporter family member 1B3
A sodium-independent organic anion transporter that functions in the uptake of various drugs and endogenous compounds including estradiol; taurocholate; leukotriene c4; and methotrexate.
Solute carrier organic anion transporter family member 2B1
Solute carrier organic anion transporter family member 2B1 is encoded by the human SLCO2B1 gene. This protein is involved in transport of organic anions and may function in regulation of placental uptake of sulfated steroids.
Solute carrier family 22 member 1 is encoded by the human SLC22A1 gene. This protein is involved in bidirectional cation transport.
Steroid transmembrane transporter SLC22A24
A protein that is a translation product of the human SLC22A24 gene.
A protein that is a translation product of the human UGT1A1 gene.
A protein that is a translation product of the human UGT1A3 gene.
A protein that is a translation product of the human UGT1A4 gene.
UDP-glucuronosyltransferase 1-6 is encoded by the human UGT1A6 gene. This protein is involved in the elimination of phenolic metabolites.
A protein that is a translation product of the mouse Ugt1a7c gene.
A protein that is a translation product of the human UGT1A8 gene.
A PPAR alpha and PPAR gamma target gene. The enzyme plays an important role in elimination and detoxification of drugs, xenobiotics, and metabolizing endogenous compounds, including catecholestrogens and fibrates.
A protein that is a translation product of the human UGT1A10 gene.
A protein that is a translation product of the human UGT2B4 gene
UDP-glucuronosyltransferase 2B7 is encoded by the human UGT2B7 gene. This protein plays a role in regulating the metabolism of estrogen metabolites.
A protein that is a translation product of the human UGT2B10 gene.
UDP-glucuronosyltransferase 2B15 is encoded by the human UGT2B15 gene. This protein is involved in the catabolism of xenobiotics and steroids.
A protein that contains a C-terminal UDPGT domain that in active form catalyzes the transfer of glucuronic acid to a wide variety of exogenous and endogenous lipophilic substrates.
A protein that is a translation product of the SLC10A1 gene
UDP-glucuronosyltransferase 2B17 is encoded by the human UGT2B17 gene. This protein plays a role in the metabolism of steroids and xenobiotics.
Opioid Drug Ontology (ODO) (https://opioiddrugontology.github.io/) - Nicolette Ross (https://orcid.org/0000-0002-4677-2140)
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Multidrug resistance-associated protein 2
The multidrug resistance protein 2 (MRP2; ABCC2) is an ATP-binding cassette transporter accepting a diverse range of substrates, including glutathione, glucuronide, and sulfate conjugates of many endo- and xenobiotics.
Joan Glenny Pescov (https://orcid.org/0009-0008-8186-7058)