Hello,
I got reviver comment " please look into the comparative assessments regarding Ki (inhibition constant); Kd (dissociation constant), and Km "equilibrium constant" of the target protein before vs after docking". Can someone suggest me how to calculate the values for Ki (inhibition constant); Kd (dissociation constant), and Km "equilibrium constant. Thanks
The dissociation constant (Kd) of an inhibitor is generally the same as the inhibition constant (Ki).
Km is not, generally, the same as an equilibrium constant for substrate binding, although it can be in some cases. Km is the concentration of the substrate that results in half the maximal rate (Vmax) of catalysis.
Km is measured by Michaelis-Menten analysis, in which the initial rate of catalysis is measured as a function of substrate concentration, and the resulting data are fit to the Michaelis-Menten equation. This is a straightforward process for a single-substrate enzyme reaction, but is more complex when the reaction involves more than one substrate.
Measuring Ki requires knowing the kinetic mechanism of the reaction, the kinetic mechanism of inhibition, and the substrate Km (or Kms in the case of multiple substrate reactions).
In the simplest cases, for single-substrate reactions, the relationship between Ki and Km takes a simple mathematical form that depends on the mode of inhibition, allowing Ki to be determined experimentally by enzyme kinetics or by measuring the concentration of inhibitor that causes 50% inhibition (IC50). This is also true for more complex enzyme reactions, but the mathematical relationships are more complicated. Ki can also be measured by some type of equilibrium binding experiment.
K value during docking reproduce by autodock4
Use autodock4 to perform docking and get k value
To calculate Ki, conduct enzyme inhibition assays with varying substrate and inhibitor concentrations, then analyze the data using Lineweaver-Burk or Dixon plots. For Kd, employ techniques like isothermal titration calorimetry or surface plasmon resonance to measure ligand binding at different concentrations, then fit the data to a binding curve. To determine Km, perform enzyme kinetics experiments with varying substrate concentrations, plot the results as a Michaelis-Menten curve, and use regression analysis to find Km. Compare these values before and after docking by measuring them for the unbound protein, conducting docking simulations, then re-evaluating for the docked complex.