Nucleic Acids Research Advance Access originally published online on April 24, 2009
Nucleic Acids Research 2009 37(Web Server issue):W441-W445; doi:10.1093/nar/gkp253
Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W441-W445
Published by Oxford University Press 2009
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
R. Z. Cer1,
U. Mudunuri1,
R. Stephens1 and
F. J. Lebeda2,*
1Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA and 2US Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702-5011, USA
*To whom correspondence should be addressed. Tel: +1 301 619 4279; Fax: +1 301 619 2348; Email: frank.lebeda{at}amedd.army.mil
Received February 6, 2009. Revised March 25, 2009. Accepted April 5, 2009.
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ABSTRACT
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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
user-defined 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).
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INTRODUCTION
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Some analyses of networks, pathways and metagenomics focus on
identifying key proteins or polynucleic acids as targets for
inhibitory compounds. Typically, high-throughput screening assays
are initially used to compare and down-select potential inhibitors
of enzymatic activity or macromolecule-ligand binding. Many
functional assays seek a total inhibitor concentration that
reduces these activities by 50% (
IC50). However, the
IC50 value
depends on concentrations of the enzyme (or target molecule),
the inhibitor, and the substrate (or ligand) along with other
experimental conditions. What is required is an accurate determination
of the
Ki value, an intrinsic, thermo-dynamic quantity that
is independent of the substrate (ligand) but depends on the
enzyme (target) and inhibitor. Thus, comparisons can be more
readily made among different laboratories to characterize the
inhibitors. While these more time-consuming assays are usually
done with the most promising candidates, accurate, initial estimates
of
Ki values for more of the candidates would be beneficial.
A much discussed problem in the literature (
1–8) is converting
IC50 to
Ki values because even the simplest types of inhibitory
mechanisms (e.g. competitive, uncompetitive and noncompetitive)
will influence the calculation.
To help address this problem, our web-server tool calculates Ki values from IC50 values using equations for enzyme-substrate and target-ligand interactions by different inhibitory mechanisms (http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp). Additional calculations are performed for tightly bound inhibitors of enzyme-substrate reactions in which free, rather than total, concentrations of the molecular species are calculated for nonclassic Michaelis–Menten kinetics. Similar calculations can be performed for target molecule-ligand systems. User-defined input values include total concentrations of the enzyme (or target molecule) and substrate (or ligand), the Km of the enzyme-substrate (or the Kd of the target-ligand) reaction and the IC50 value. The outputs include tabulations of the Ki values under different kinetic schemes, extensive tabulations of the results, summary histograms and the corresponding equations. Help buttons are available for Background, Assumptions, Literature, Links and Equations along with examples taken from the host database-server that contains kinetic information on neurotoxin inhibitors. An example calculation is included here for a tight-binding inhibitor of an enzyme–substrate reaction, while other enzyme inhibitor and protein–ligand–inhibitor examples are also provided. Our rationale for creating this converter is to enable end users to judge the quality of the underlying assumptions for these calculations and to help facilitate research and the development of potential therapeutic products.
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METHODS
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Reactions and equations
The website cited in (
9) served as an initial design template
for our
IC50-to-
Ki converter. Equations (1–4) were adapted
from refs. (
3), (
6) and (
9) whereas we derived Equation (
5)
for this study. The analytic expressions for
Ki that are shown
below were verified numerically by methods used in a previous
kinetic analysis (
10).
The derivations for converting IC50 to Ki values published by Brandt et al. (3) include three types of classic inhibitor mechanisms in which different relations may exist between S and Km. For tightly bound inhibitors, the equation for Ki by Copeland et al. (6) is used to take into account the larger amounts of inhibitor bound species, thus making the Michaelis–Menten assumption of the total enzyme concentration being equal invalid (5). These equations are also relevant for protein–ligand–inhibitor (P–L–I) interactions that also adhere to the above assumptions.
Enzyme–substrate–inhibitor reactions
For competitive inhibition
where
Kd =
k–1/
k1 and
Ki =
k–i/
ki, the classic
expression is
 | (1a) |
and
for tightly bound inhibitors (
5,
6)
 | (1b) |
For uncompetitive inhibition
the classic expression is:
 | (2a) |
and for tightly bound inhibitors (
5,
6)
 | (2b) |
For noncompetitive
inhibition (
2)
where
Kia =
k–ia/
kia and
Kib =
k–ib/
kib, the classic expression
is:
 | (3a) |
and for tightly
bound inhibitors (
5,
6)
 | (3b) |
This noncompetitive reaction also assumes that the inhibitor
dissociation constants are equal:
Kia =
Kib =
Ki. Mixed inhibition,
where
Kia < >
Kib, is not considered here.
P–L–I reactions
For total concentrations, E is replaced by P and S is replaced by L. Additional reaction schemes are located at this tool's website. As in classic enzyme–substrate systems the relation of Ki and IC50 in competitive inhibition is:
 | (4a) |
For protein–ligand experiments with
tight-binding inhibitors, the free rather than the total concentrations
of the reactants need to be used as modified from ref. 9
 | (4b) |
where
I50 and
L50 are the free concentrations
of the inhibitor and ligand, respectively, at 50% inhibition,
and
P0 is the free concentration of the protein in the absence
of inhibitor. The concentration of the free inhibitor species
is given by
 | (4c) |
where
P0 = –((
Kd +
L–
P) + [(
Kd +
L–
P)
2 + 4
PKd]
1/2)/2,
PL0 =
P–
P0,
PL50 =
PL0/2,
L0 =
L–
PL0 and
L50 =
L–
PL50.
For this study, we derived a corresponding value of Ki for uncompetitive inhibition
 | (5) |
in
which the variables are the same as in Equation (4) except that
L50 = – ((
P–
L) + [(
P–
L)
2 + 4(
PL0Kd/2)]
1/2)/2.
Although in this study we use the term
Kd to quantify an antagonist's
effect, the pharmacology-derived EC
50 value is more appropriate
when functional experiments are performed (
11).
General assumptions and caveats
It is assumed that all of the substrate- and inhibitor-binding reactions are reversible and that they all have a one-to-one stoichiometry, i.e. no multiple binding of inhibitor molecules or any form of cooperativity, or other complex mechanisms of inhibition such as partial or mixed types (3). It is also assumed that in the enzymatic reactions enzyme autocleavage did not occur and that when substrates for fluorescence resonance energy transfer were used, appropriate corrections for inner filter effects were performed. Comparison of Km or IC50 values for a set of inhibitor candidates is only assumed to be valid when they are evaluated under identical experimental conditions. In most experimental studies of enzyme kinetics, the total concentrations of substrate and inhibitor used are in excess of the enzyme concentration to make their free and total concentrations essentially the same (1). Under the conditions of some ligand-receptor (e.g. protein)-binding studies, the free concentrations also become sufficiently important to require modifications of these equations (1, 2), and (9).
Description of the web server
The IC50-to-Ki tool is implemented as a web resource using an Oracle database (Oracle9i Enterprise Edition Release 9.2.0.4
[EC]
.0), Java (JDK 1.5.0) and Apache web server components including Tomcat 4.1. Information on candidate inhibitors of the botulinum neurotoxins was collected by mining the biomedical literature including searches with botXminer (12) using the National Library of Medicine's MEDLINE®/PubMed® (13). Experimental data (IC50 values) and accompanying assay information were manually extracted from primary literature results and other relevant databases: JCVI-Pathema-Clostridium (13), Brenda (14) and Protein Data Bank (15).
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USAGE
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An internal link to the user-accessible converter is also located
on the left side of the BotDB home page. The four required inputs
for
E,
S,
Km and
IC50 are indicated with default settings for
several examples. After submitting these values by using the
‘calculate’ button, these input data are returned
along with the
Ki results for the example cases.
An illustration is provided for a tight-binding inhibitor of an enzyme–substrate (E–S) reaction (Figure 1). The values for this example are from data using cimoxatone, a tight-binding inhibitor of monoamine oxidase (16). The four inputs for E, S, Km and IC50 are 0.021, 100, 108 and 0.017, respectively, in micromolar units. The Ki results for three modes of inhibition are returned on a new page. The top block of results corresponds to the solutions for a classic inhibitor (i.e. Michaelis–Menten kinetics). The second block represents the corrections made to the first set of equations [Equations (1b–3b)] for tightly bound inhibitors when there is substantial inhibitor depletion (5,6). Equations can be viewed by clicking on a label for a mode of inhibition. Below these two tables, histograms plotting the six results are shown for a visual comparison. In this example, the results from the classic and corrected equations are quite different. This difference in Ki values enables the user to conclude that not all of the assumptions underlying classic Michaelis–Menten equations are being obeyed and that the data are consistent with the kinetics of a tight-binding inhibitor.
View larger version (52K):
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[in a new window]
[Download PowerPoint slide]
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Figure 1. Results page from the IC50-to-Ki web tool for a tight-binding inhibitor of monoamine oxidase. The top table contains sample input data obtained from ref. 16. The middle table contains the results for a classic inhibitor that follows Michaelis–Menten kinetic Equations (1a–3a) for three kinetic reactions. The bottom table contains the results for nonclassic, tight-binding inhibitor uses Equations (1b–3b) for the same three reactions. The histograms summarize these results. Equations for each displayed mode of inhibition can be viewed by clicking on its label. A help list located on the upper right side is available for more detailed information about this tool.
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Two other examples of enzyme inhibitors are also available for
users to examine at the
IC50-to-
Ki tool website. For classic
inhibition, data values using a candidate inhibitor of botulinum
neurotoxin type A (
17) are used as inputs:
E,
S,
Km and
IC50 (in micromolar units) 0.0067, 300, 1300 and 3.2, respectively.
In contrast to the tight-binding inhibitor example, the returned
values for
Ki are similar for classic and tight-binding kinetics
indicating that this data set is consistent with classical kinetics.
In another example of a potentially cooperative inhibitor of CYP3A4 (18), the input data for E, S, Km and IC50, in micromolar units, are 0.1, 50, 51 and 0.05, respectively. This example returns an error message from the converter that states that the 1:1 stoichiometry assumption may have been violated and requests the user to enter different values.
Finally, Equations (4) and (5) are used to calculate Ki values for reactions involving inhibitors of P–L-binding reactions. For this case, a user interface similar to the enzyme–substrate page is produced (see website). The values for a tight-binding inhibitor of an apoptosis-related protein from ref. 9 are used as an example calculation. The inputs are labeled P, L, Kd and IC50. In this case, only the competitive and uncompetitive modes of inhibition are considered. The tabulated output includes the free concentrations of protein and ligand species in the absence of an inhibitor (P0 and L0, respectively). The free concentrations at 50% inhibition are also returned for the protein, ligand, inhibitor, protein–ligand complex and P–L–I complex (P50, L50, etc.). As with the tight-binding enzyme inhibitor calculations, the summary histograms again indicate that these data are consistent with the kinetics of a tight-binding inhibitor.
It is our intent for this general tool to provide results for classic and tight-binding inhibitors of enzyme activity and ligand-binding reactions that are assumed to follow relatively simple kinetic schemes. These different sets of kinetic results will allow investigators to decide whether additional experiments are required to understand better the kinetic behaviors of their candidate inhibitors for further research or therapeutic product development.
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FUNDING
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The Defense Threat Reduction Agency Joint Science and Technology
Office-Chemical Biological Defense (project 3.10043_07_RD_B
to F.J.L.); and by the National Cancer Institute, National Institutes
of Health (contract No. HHSN261200800001E). Funding for open
access charge: Defense Threat Reduction Agency.
Conflict of interest statement. None declared.
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ACKNOWLEDGEMENTS
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The authors thank Drs. James J. Schmidt, John H. Cardellina
and S. Ashraf Ahmed for their insightful comments on early drafts
of this manuscript. Opinions, interpretations, conclusions and
recommendations are those of the authors and are not necessarily
endorsed by the US Army. The content of this publication does
not necessarily reflect the views or policies of the Department
of Health and Human Services, nor does mention of trade names,
commercial products, or organizations imply endorsement by the
US Government.
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ABSTRACT
INTRODUCTION
