Question

2. Many of the examples in this module refer to parameters such as Ki, IC50, Kd, logP, logD, and pKa. Explain what each of these terms refers to and what effects high or low values may have on SAR.

3 .What is meant by "acidic drug" or "basic drug" and why are these properties of importance in drug design (Hint: see optional reading)?

4. Hydrogen bonding is an important consideration in drug design. a) Describe which functional groups may be involved in hydrogen bonding and how you would test if hydrogen bonding was important in drug activity. Illustrate with chemical diagrams. b) What are internal hydrogen bonds and why would you exploit them? Draw out an example from the week's contents and illustrate your point.

5. Explain the concept of rigidification in drug design. Use a few examples.

Answer 1

The Inhibitory Constant (Ki)

• The inhibitory constant (Ki) and the IC50 of a drug that is known to cause inhibition of a cytochrome P450 (CYP) enzyme have to do with the concentration needed to reduce the activity of that enzyme by half. More specifically the Ki is reflective of the binding affinity and the IC50 is more reflective of the functional strength of the inhibitor for a drug. Since the Ki takes into account the IC50 is its calculation, the Ki is being reported more often by drug companies.
• For noncompetitive inhibition of enzymes, the Ki of a drug is essentially the same numerical value as the IC50, whereas for competitive and uncompetitive inhibition the Ki is about one-half that of the IC50's numerical value.  
• The smaller the Ki, the greater the binding affinity and the smaller amount of medication needed in order to inhibit the activity of that enzyme. If a Ki is much larger than the maximal drug concentrations that a patient is typically exposed to from typical dosing, then that drug is not likely to inhibit the activity of that enzyme.

If clinicians have not already started to encounter Ki's in the literature and product package inserts for medications, they will likely encounter them in the future.1-3 The Ki, in part, becomes important for helping to predict clinically relevant drug interactions.1,3 Simply stated, the inhibitory constant (Ki) and the half maximal inhibitory concentration (IC50) of a drug that is known to cause inhibition of a cytochrome P450 (CYP) enzyme have to do with the concentration needed to reduce the activity of that enzyme by half. More specifically the Ki is reflective of the binding affinity and the IC50 is more reflective of the functional strength of the inhibitor, but both factor in the concentration of drug present to inhibit the enzyme activity. Of note, for drugs that are noncompetitive inhibitors of CYP enzymes, the Ki of a drug is essentially the same numerical value as the IC50's numerical value, whereas for competitive and uncompetitive inhibition the Ki is about one-half that of the IC50.3 Therefore, the smaller the Ki, the smaller amount of medication needed in order to inhibit the activity of that enzyme.

If a Ki is much larger than the maximal plasma drug concentrations a patient is exposed to from typical dosing, then that drug is not likely to inhibit the activity of that enzyme. This effect can also be reflected in the [I]/Ki ratio.1 A clinically relevant example of this can be seen by evaluating the Ki for proton pump inhibitors (PPIs) on cytochrome P-450 (CYP) 3A4 enzyme.4 In this example, the Ki's are significantly higher for most PPIs (42 to 51 mM) than their respective maximum concentrations (1 to 5.2 mM) in patients who are either extensive metabolizers or poor metabolizers of 2C219.4-9 Because the Ki's for PPIs is so much greater than the maximal drug concentrations seen with typical dosing, most PPIs are not likely to inhibit the activity of CYP3A4.

It is also important to recognize when interpreting or when reviewing the Ki for a particular medication that a few factors are known to influence the value obtained from a study. Those factors include specificity of the substrate, the binding components in the incubation system and any substrate or inhibitor depletion.1 As it relates to the incubation system, depending on the biologic system used, the Ki can fluctuate resulting in a range for the Ki.4,10

Therefore, the use of the Ki is helpful in designating the likelihood that a particular medication is going to inhibit a particular enzyme and result in a clinically relevant drug interaction with a substrate for the enzyme. In many cases, the evaluation of the Ki in relation to the concentration of the inhibitor present in the body has already been done and is used as the basis for programs or certain drug information sources to report a particular medication as an inhibitor or not. It is equally important for clinicians to also recognize that all medications may or may not have been fully evaluated depending upon their arrival into the market. In such cases or situations, when trying to discern the likelihood of a drug interaction occurring between coadministered medications, clinicians may need to resort to this method of evaluation.

The half maximal inhibitory concentration (IC₅₀)

It is a measure of the effectiveness of a substance in inhibiting a specific biological or biochemical function.This quantitative measure indicates how much of a particular drug or other substance (inhibitor) is needed to inhibit a given biological process (or component of a process, i.e. an enzyme, cell, cell receptor or microorganism) by half. The values are typically expressed as molar concentration. It is commonly used as a measure of antagonist drug potency in pharmacological research. According to the FDA, IC₅₀ represents the concentration of a drug that is required for 50% inhibition in vitro.It is comparable to an EC₅₀ for agonist drugs. EC₅₀ also represents the plasma concentration required for obtaining 50% of a maximum effect in vivo.

K_D value: a quantitative measurement of antibody affinity

K_D​ is the equilibrium dissociation constant, a ratio of k_off/k_on, between the antibody and its antigen. K_D and affinity are inversely related. The K_D value relates to the concentration of antibody (the amount of antibody needed for a particular experiment) and so the lower the K_D value (lower concentration) and thus the higher the affinity of the antibody.

Lipophilicity (logD, logP)

Lipophilicity tells about the compounds ability to dissolve into lipohilic (non-aqueous) solutions. Lipophilicity is needed for the compounds to permeate through the various biological membrane. Lipophilicity is typically measured as the compounds distribution between non-aqueous (octanol) and aqueous (water) phase and the result is expressed as a 10-base logarithm of the concentration ratios between these phases (partition coefficient), logP. A desired logP value (octanol-water partition coefficient) is no more than 5 (also part of the so-called Lipinski rule-of-five; logP 5 = 1:100,000 concentration difference between water and octanol phases).

Another common measure for lipophilicity is the distribution coefficient, logD. lodD takes into account the compounds ionized and non-ionized forms, and therefore the measurement is done at different pH. For un-ionizable compounds, log P = log D at any pH and on the other hand, logP is the octanol-water partition for the neutral (un-ionized) form of the compound. Amongst the different pH values, typically the most interesting is pH 7.4, the physiological pH value.

pKa

The acid dissociation constant, Ka, is a mesure of the strength of the acid and its typically expressed as pKa (-log10(ka). Drug compounds are almost always weak acids or bases and depending on the pH, they are thus either charged (A- or HB+) or neutral. The neutral form has better lipophilicity and thus better permeability whilst the charged form has better aqueous solubility. pKa values gives the pH above which the compound is neutral (bases; B) or charged (acids; A-) and below which the compound is neutral (acids; HA) or charged (bases; HB+)