IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
TLDR
A new web-server tool estimates Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands to enable end users to help gauge the quality of the underlying assumptions used in these calculations.Abstract:
A new web-server tool estimates Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules (e.g. proteins, polynucleic acids) and ligands. This converter was developed to enable end users to help gauge the quality of the underlying assumptions used in these calculations which depend on the type of mechanism of inhibitor action and the concentrations of the interacting molecular species. Additional calculations are performed for nonclassical, tightly bound inhibitors of enzyme-substrate or of macromolecule-ligand systems in which free, rather than total concentrations of the reacting species are required. Required userdefined input values include the total enzyme (or another target molecule) and substrate (or ligand) concentrations, the Km of the enzyme-substrate (or the Kd of the target-ligand) reaction, and the IC50 value. Assumptions and caveats for these calculations are discussed along with examples taken from the literature. The host database for this converter contains kinetic constants and other data for inhibitors of the proteolytic clostridial neurotoxins (http:// botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp).read more
Citations
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Journal ArticleDOI
Structure and Activity of Paenibacillus polymyxa Xyloglucanase from Glycoside Hydrolase Family 44
Antonio Ariza,Jens M. Eklöf,Oliver Spadiut,Wendy A. Offen,Shirley M. Roberts,Werner Besenmatter,Esben Peter Friis,Michael Skjøt,Keith S. Wilson,Harry Brumer,Gideon J. Davies +10 more
TL;DR: The biochemical characterization of the endo-β-1,4-(xylo)glucan hydrolase from Paenibacillus polymyxa with polymeric, oligomeric, and defined chromogenic aryl-oligosaccharide substrates shows an unusual specificity on defined xyloglucan oligosacbarides, cleaving the XXXG-XXXG repeat into XXX and GXXXG.
Journal ArticleDOI
Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.
James J. Valdés,Alexandra Schwarz,Israel Cabeza de Vaca,Israel Cabeza de Vaca,Eric Calvo,Joao H. F. Pedra,Victor Guallar,Victor Guallar,Michalis Kotsyfakis +8 more
TL;DR: It is shown that tryptogalinin is phylogenetically related to a Kunitz peptide from Rhipicephalus appendiculatus, also reported to have a high affinity for β-tryptase, which allows for hypothesizing about the molecular basis of this function at the atomic level.
Journal ArticleDOI
The Reliability of Estimating Ki Values for Direct, Reversible Inhibition of Cytochrome P450 Enzymes from Corresponding IC50 Values: A Retrospective Analysis of 343 Experiments
Lois J. Haupt,Faraz Kazmi,Brian W. Ogilvie,David B. Buckley,Brian D. Smith,Sarah Leatherman,Brandy L. Paris,Oliver T. Parkinson,Andrew Parkinson +8 more
TL;DR: Results suggest that, under appropriate experimental conditions with the substrate concentration equal to Km, values of Ki for direct, reversible inhibition can be reliably estimated from values of IC50/2.
Journal ArticleDOI
Novel adamantane-pyrazole and hydrazone hybridized: Design, synthesis, cytotoxic evaluation, SAR study and molecular docking simulation as carbonic anhydrase inhibitors
TL;DR: A series of pyrazole derivatives 4, 5, 6, 12, 13, 14 as well as hydrazone derivatives 7, 10, 11 were synthesized starting from adamantane-1-carbohydrazide as the bioactive core.
Journal ArticleDOI
Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for ¹⁹F NMR studies.
Marek R. Baranowski,Anna Nowicka,Anna M. Rydzik,Marcin Warminski,Renata Kasprzyk,Blazej A. Wojtczak,Jacek Wójcik,Timothy D. W. Claridge,Joanna Kowalska,Jacek Jemielity +9 more
TL;DR: It is found that fluorophosphate nucleotide analogues can be used to monitor activity of enzymes with various specificities and metal ion requirements, including human DcpS enzyme, a therapeutic target for spinal muscular atrophy.
References
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Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction.
TL;DR: The analysis described shows K I does not equal I 50 when competitive inhibition kinetics apply; however, K I is equal to I 50 under conditions of either noncompetitive or uncompetitive kinetics.
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Development and optimization of a binding assay for the XIAP BIR3 domain using fluorescence polarization
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TL;DR: The development of a homogeneous high-throughput assay based on fluorescence polarization for measuring the binding affinities of small-molecule inhibitors to the BIR3 domain of XIAP and results obtained indicated that the FP-based competitive binding assay performs correctly as designed.
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A linear equation that describes the steady-state kinetics of enzymes and subcellular particles interacting with tightly bound inhibitors.
TL;DR: D dose-response measurements generate a linear plot of inhibitor concentration divided by degree of inhibition against velocity without inhibitor divided by velocity with inhibitor, which indicates that the inhibitors of oxidative phosphorylation, rutamycin and bongkrekic acid, are tightly bound to rat liver mitochondria.
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BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
TL;DR: The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced and a new search option provides the access to protein-specific data.
Journal ArticleDOI
Fluorescence Polarization Competition Assay: The Range of Resolvable Inhibitor Potency Is Limited by the Affinity of the Fluorescent Ligand
TL;DR: The higher the affinity of the fluorescent ligand, the wider the range of inhibitor potency that can be resolved, and an approximate estimate for the low end of inhibitor K(i) values thatCan be resolved is the K(d) value of theorescent ligand.