Medicinal Chemistry — Understanding Enzyme Kinetics

Here, we continue our understanding of drug targets, this time focusing on enzyme kinetics.

Enzymes are biological macromolecules that act as catalysts in biochemical reactions. The metabolic processes and chemical reactions that sustain life often involve enzymes. Enzymes basically decrease the Gibbs free energy of activation (ΔG), accelerating the rate of reaction. The majority of enzymes are proteins, and proteinaceous enzymes will be the focus of this section. Catalytic RNA molecules are also known and they are referred to as ribozymes. Just like other proteins under normal conditions, proteinaceous enzymes adopt certain three dimensional conformations that are crucial to their activity. Enzymes sometimes recruit other organic molecules or inorganic cofactors which may be essential to catalytic activity. An enzyme's substrate is the molecule upon which enzymes act. In biochemistry, the suffix -ase is used to name the majority of enzymes.

As drug targets, enzymes are highly important. Enzyme inhibition has many applications. Many enzymes can be inhibited to treat a vast range of medical conditions. HMG-CoA reductase inhibitors as an example were described in a previous article. Other examples of drugs that act on enzymes include the antimalarial compound pyrimethamine (dihydrofolate reductase inhibitor), clavulanic acid (β-lactamase inhibitor), and the antineoplastic agent lapatinib (dual tyrosine kinase inhibitor).

Pyrimethamine-Clavulanic Acid-Lapatinib

Introduction to Michaelis-Menten Kinetics

Enzyme kinetics is the study of enzyme-catalysed chemical reactions. Enzymes are highly efficient catalytic systems. Generally, they can enhance reaction rates by a factor of 105 - 1017. Studying the kinetics of enzyme-catalysed reactions can be useful in determining an enzyme inhibitor’s properties. Michaelis-Menten kinetics is a widely known and useful model of enzyme kinetics. The model was named after Leonor Michaelis and Maud Menten, the individuals who described the mathematical model relating reaction rate and substrate concentration [S]. In chemistry, square brackets are often used to denote concentration (for example, [X] means ‘concentration of X’). Square brackets are also used when describing coordination complexes.

The site where substrate molecules binds to the enzyme and undergoes chemical reactions is referred to as the active site (sometimes referred to by some as the orthosteric site). Sites other than a protein's active site are referred to as the allosteric site. Inhibitors can bind to the active site or to an allosteric site. Enzyme inhibitors that are able to form covalent bonds with the enzyme are referred to as irreversible inhibitors. Inhibitors that bind to active sites through intermolecular bonds are called reversible inhibitors. Reversible inhibitors are divided into:

  • Competitive Inhibition
  • Uncompetitive Inhibition
  • Noncompetitive Inhibition

It is important to remember that different people may use different symbols or characters in the following equations. Don’t be bothered by this. It is more important to understand the meaning of the equations. If your understanding of basic algebra and chemical kinetics is a little rusty, it would be a good idea to go over those before proceeding.

The rate of enzyme-catalysed reactions is often referred to as enzyme velocity or simply velocity. Note that enzyme velocities are typically reported at time zero. µ mol min-1 is a commonly used unit of measurement for V0. The complex formed between an enzyme and its substrate is referred to as an ES complex (enzyme-substrate complex). The Michaelis-Menten model of enzyme kinetics uses the concept of the formation of the ES complex. Under the model, the enzyme and the substrate form an ES complex. The formed ES complex can either form the product P and regenerate the enzyme, or dissociate back to E and S. The model is expressed in the equation shown below.

The formation of the product (P) from ES is assumed to be irreversible. The reaction rate constants are k1, k2, and k3.

  • k1: rate constant for the formation of ES
  • k2: rate constant for the dissociation of ES back to E + S
  • k3: rate constant for the formation of E + P

Based on studies of many enzymes, it was found that under conditions of relatively low [S], the rate increases almost linearly as [S] increases. In other words, the rate is directly proportional to [S] at relatively low [S]. At higher [S], the rate increases by smaller and smaller amounts as [S] increases until the reaction rate becomes almost constant.

Michaelis-Menten Model Graph

The shape of the curve is hyperbolic. L. Michaelis and M. Menten arrived with an equation that describes the above relationship. The equation is named the Michaelis-Menten equation and is given by:

Michaelis-Menten Equation

Note that in chemistry, the lowercase Greek letter ν (nu) is sometimes used to denote the rate of reaction. The derivation of the equation will not be shown here. As seen in the graph, ν increases as [S] increases, asymptotically approaching Vmax. When L. Michaelis and M. Menten derived the equation, a new constant, KM (Michaelis-Menten constant) was defined. K is defined as the concentration of the substrate where the reaction rate is half of the maximum reaction velocity, Vmax. The unit of measurement of KM is M. The magnitude of KM varies widely depending on the enzyme and the substrate. KM is also equal to the sum of k2 and k3 over k1.

The value of KM can also give insight on substrate binding affinity for the enzyme. High KM values usually indicate weak substrate affinity for the enzyme, whereas low KM values usually indicate strong substance affinity for the enzyme.

Lineweaver-Burk Plot

Since ν asymptotically approaches Vmax, it is extremely difficult to assess Vmax from plots of [S] against ν. The parameters of the Michaelis-Menten Equation can be determined through linearised forms of the equation such as the Lineweaver-Burk equation and the Hanes-Woolf equation. The Lineweaver-Burk plot would be the plot of 1/[S] (x-axis) against 1/ν (y-axis). As you would recall from mathematics, the equation of a straight line is y = mx + c where m is the slope of the equation and c is the constant. The Lineweaver-Burk equation has this form.

Equation of a Straight Line

Lineweaver-Burk Equation

Extracting the value of Vmax is easier because it is simply the reciprocal of the constant of the equation. Once Vmax is known, KM can be determined from the slope of the line. The x-axis intercept is equal to -1/Km and the y-axis intercept is equal to 1/Vmax. Lineweaver-Burk plots are extremely useful. They can also provide information on the type of inhibition compounds give.

Lineweaver-Burk Plot

Lineweaver-Burk Plot

Lineweaver-Burk Equation Derivation

Michaelis-Menten Equation

Rearranging the Michaelis-Menten equation gives (1)

Dividing both sides of the equation with Vmax gives (2)

Rearranging (2) gives (3)

The [S] cancels to give (4)

Rearranging (4) gives the Lineweaver-Burk equation

Lineweaver-Burk Equation

Competitive Inhibitors

Reversible competitive inhibitors compete with substrate molecules for the enzyme’s active site. These inhibitors are typically structurally similar to the substrate. Enzymes may bind to the substrate or the inhibitor but not both simultaneously. At very high [S], more substrate can bind to the enzyme and they can outcompete the inhibitor, overcoming inhibition.

Competitive Inhibitor Graph

Statins are competitive inhibitors. ACE inhibitors such as perindopril and fosinopril are other examples of competitive inhibitors. ACE inhibitors are mainly employed as antihypertensives and can be used to treat congestive heart failure.

Perindopril-Fosinopril

Uncompetitive Inhibitors

Uncompetitive inhibitors are enzyme inhibitors that bind to the ES complex. Uncompetitive inhibitors are sometimes referred to as anti-competitive inhibitors. A Lineweaver-Burk plot of uncompetitive enzyme inhibition is shown below. Lithium, a known uncompetitive inhibitor, is used to treat conditions such as manic depression.

Uncompetitive Inhibitor Graph

Noncompetitive Inhibitors

Noncompetitive inhibitors can bind to the enzyme whether or not a substrate has already been bound. Noncompetitive inhibition is a form of allosteric inhibition. It is important to mention that not all inhibitors that bind at allosteric sites are noncompetitive inhibitors. The binding of the inhibitor at an allosteric site causes an overall change of the three dimensional structure of the enzyme. The consequence of this conformational change is reduced catalytic activity.

The antidepressant, tranylcypromine is an example of a nonselective noncompetitive, irreversible inhibitor of the monoamine oxidase enzyme (MAO). Tranylcypromine is unable to distinguish between the MAO-A and MAO-B isozymes of MAO. This drug is also used as an anxiolytic agent.

Tranylcypromine

Tranylcypromine

Hanes-Woolf Plot

The Hanes-Woolf plot is another method that linearises the Michaelis-Menten equation, plotting [S] (x-axis) against [S]/ν (y-axis). Just like the Lineweaver-Burk equation, the Hanes-Woolf equation is of the form y = mx + c. The Hanes-Woolf plot is thought to be more accurate than Lineweaver-Burk for the determination of kinetic parameters. The plot and the equation are shown below.

Hanes-Woolf Plot

Hanes-Woolf Plot

Equation of a Straight Line

Hanes-Woolf Equation

Hanes-Woolf Equation Derivation

Michaelis-Menten Equation

Inverting the Michaelis-Menten Equation gives (1)

Multiplying both sides of the equation with [S] gives (2)

Rearranging (2) gives (3)

Rewriting (3) gives the Hanes-Woolf equation

Hanes-Woolf Equation

Studying enzyme kinetics can prove beneficial to understanding how drugs work at enzymes. A combination of an understanding of a drug’s mode of action and structure-activity relationships, it may be possible to apply drug design methods to improve drug activity.

Summary of Equations

Michaelis-Menten Equation Michaelis-Menten Constant

 

Lineweaver-Burk Equation Hanes-Woolf Equation

Further Reading

Chemical kinetics is described in most introductory chemistry textbooks. Enzyme kinetics is described in far greater detail in many undergraduate level biochemistry text books. Many of these books also show the derivation of the Michaelis-Menten equation.
Fundamentals of Enzyme Kinetics 4th Edition

  • A. Cornish-Bowden, © 2012 Wiley-VCH Verlag & Co. KGaA, Weinheim, Germany.

Enzyme Kinetics: Principles and Methods 2nd Edition

  • H. Bisswanger, © 2008 Wiley-VCH Verlag & Co. KGaA, Weinheim, Germany.

Quantum Mechanical Methods for Enzyme Kinetics

  • Annu. Rev. Phys. Chem., 2002, 53, pp 467-505.
By | 2016-12-16T13:51:07+00:00 December 2nd, 2014|Medicinal Chemistry|0 Comments

About the Author:

Jordan K.M.

Leave A Comment

error: Content is protected !!