Enzyme Inhibitors

Routes to Rational Drug Design

Topics For Discussion

What are Enzymes

How do Enzymes work

How do we study enzymes

What are Enzyme Inhibitors

How does understanding how an enzyme works allow the rational design of drugs

What Are Enzymes

• Protein

• Catalyst

• Responsible for nearly all of the chemical reactions that take place in a living cell

What is a Catalyst

• Accelerate the rate of a chemical reaction

• Are not consumed by the reaction

Rates of Chemical Reaction

• What determines the rate of a chemical reaction?

Reaction Rates

• First… what determines if a reaction goes at all?

• Must consider the ΔG for the reaction

Reaction Coordinate

Gib

bs

Fre

e E

ne

rgy

Conversion of S to P

S

P

Reaction Direction

• Reactions only proceed spontaneously in the direction given if the ∆G is negative

• But just because the reaction is spontaneous, doesn’t mean that it goes at any measurable rate

Transition State Theory

• Consider the conversion of S to P• -dS/dt = k[S]• Transition state theory proposes that in the

[S] there is a distribution of energetic forms and one such form is referred to as the transition state between S and P.

• The reaction only proceeds through this form

Transition State Theory

• So that the rate of the reaction really is

-dS/dt = k[S*] where S* is the transition state.

[S*]

• So how much [S*] is present

K* = [S*]/[S] where K* is the equilibrium constant between the transition state and the ground state

Transition State Concentration• So one can express the [S*] as a function of

the K* and the [S] [S*] = K*[S]

• And since ΔG* = -RTlnK*• [S*] = e- ΔG*/RT [S]• And therefore the rate of the reaction would

be -d[S]/dt = ke- ΔG*/RT [S]• The term in red is the rate constant for the

reaction.

• G = free energy at any moment

• G0 = standard-state free energy

• R = ideal gas constant = 8.314 J/mol-K

• T = temperature (Kelvin)

Reaction Rate

• Therefore the magnitude of the ∆G* determines the rate of the reaction

• The lower this value is the faster the reaction goes

• Therefore, for an enzyme to catalyze a reaction it must lower the transitions state free energy (transition state activation energy)

Consider this Reaction

Why does the reaction go slowly?

What Could Help the Reaction Go Faster

What Else Could Make It Go Faster

But High Acid Concentrations are not “Biological”

Where Do These General Acids/General Bases and

Electrostatic Groups Come From

Proteins are linear polymers of amino acids

Some of the Amino Acids have side chains with functional groups.

Another Way to Accelerate a Reaction

Covalent Nucleophilic Catalysis

The reaction mechanism has changed

Forms a covalent intermediate

But at the end the reaction is the same

How Enzymes Catalyze Reactions

• General acid/general base

• Electrostatic

• Change the reaction mechanism

• Proximity and orientation effects

• Entropy considerations

How Do We Study Enzymes

Enzyme Kinetics

Enzymatic Reactions

• Enzyme = E

• Substrate = S

• Product = P

• Velocity = ΔP/ ΔT (where T = time)

E + S → P

Michaelis Menten Equation

Also: 1/v = (Km + S)/Vmax(S)

or = Km/Vmax + 1/Vmax

Inhibitors

• Why would you want to inhibit an enzyme

• What are the different kinds of enzyme inhibitors

• How can you know what kind of inhibitor a molecule is

Competitive Inhibition

Non-competitive Inhibition

Uncompetitive Inhibition

What Kind of Inhibition would this Compound Give?

• Competitive?

• Non-competitive?

• Un-competitive?

• Other?

Transition State Analogues

Saqinivir bound to HIV protease