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
Characterization of peptides from common bean protein isolates and their potential to inhibit markers of type‐2 diabetes, hypertension and oxidative stress
TL;DR: Peptides from common bean have antidiabetic and antihypertensive potential regardless of their antioxidant capacity.
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Modulation of Starch Digestion for Slow Glucose Release through “Toggling” of Activities of Mucosal α-Glucosidases
Byung-Hoo Lee,Razieh Eskandari,Kyra Jones,Kongara Ravinder Reddy,Roberto Quezada-Calvillo,Buford L. Nichols,David R. Rose,Bruce R. Hamaker,B. Mario Pinto +8 more
TL;DR: The results support the prospect of controlling starch digestion rates to induce slow glucose release through the toggling of activities of the mucosal α-glucosidases by selective enzyme inhibition.
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Mechanism of Inhibition of the Human Sirtuin Enzyme SIRT3 by Nicotinamide: Computational and Experimental Studies
TL;DR: A model for base exchange inhibition that relates such kinetic properties to physicochemical properties, including the free energies of enzyme-ligand binding, is reported, and the latter is estimated through the first reported computational binding affinity calculations for SIRT3:NAD+, SIRT 3:NAM, and analogous complexes for Sir2.
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Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers.
TL;DR: Combining contact-quenched fluorogenic probes with orthogonal DNB (the quencher-binding RNA aptamer) and SRB-2 aptamers (a fluorophore-binding RNAs) allowed dual-colour imaging of two different fluorescence-enhancing RNA tags in living cells, opening new avenues for studying RNA co-localization and trafficking.
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Bromo-deaza-SAH: A potent and selective DOT1L inhibitor
Wenyu Yu,David Smil,Fengling Li,Wolfram Tempel,Oleg Fedorov,Kong T. Nguyen,Yuri Bolshan,Rima Al-awar,Stefan Knapp,Cheryl H. Arrowsmith,Masoud Vedadi,Peter Brown,Matthieu Schapira,Matthieu Schapira +13 more
TL;DR: The addition of a single halogen atom at a critical position in the cofactor product S-adenosylhomocysteine (SAH, an inhibitor of SAM-dependent methyltransferases) results in an 8-fold increase in potency against DOT1L, and reduced activities against other protein and non-protein methyl transferases.
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
Zaneta Nikolovska-Coleska,Renxiao Wang,Xueliang Fang,Hongguang Pan,York Tomita,Peng Li,Peter P. Roller,Krzysztof Krajewski,Naoyuki G. Saito,Jeanne A. Stuckey,Shaomeng Wang +10 more
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.
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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.