PharmSci 177/277 Lecture 3: Drugs and Enzymes

Lecture 3: Drugs and Enzymes

• Lecture given by Prof. Trader in PharmSci 177/277 and Chem 177 during Winter 2025.

Key Concept of Enzymes

• Enzymes convert substrates to products.
• Shape complementarity is crucial for enzyme activity. This means the enzyme's shape matches the shape of the substrate, like a lock and key.
• Enzymes lower the activation energy needed for a reaction, allowing it to proceed faster.
• This is shown graphically through energy diagrams comparing enzymatic and non-enzymatic reactions.

What Enzymes Do

• Enzymes provide a reaction surface (active site).
• Enzymes create a suitable environment, often hydrophobic, for the reaction.
• Enzymes bind reactants together, positioning them correctly for the reaction.
• Enzymes weaken bonds in reactants through coordination or strain.
• Enzymes facilitate acid/base catalysis.
• Enzymes provide nucleophilic groups for reactions.
• Enzymes stabilize the transition state using intermolecular bonds.

Classifications of Enzymes

• Enzymes are classified by EC numbers.
• EC numbers delineate the type of reactions catalyzed by enzymes.
• Different classes of enzymes catalyze different types of reactions like oxidations, reductions, group transfers, hydrolysis, etc.

Substrate Binding-Induced Fit

• Enzyme binding induces a conformational change in the enzyme.
• Enzyme-substrate binding interactions must be strong enough to hold the substrate for conversion to product and weak enough for product release.
• Binding maximizes intermolecular forces.
• The binding process can induce strain in the substrate bonds to facilitate reaction.

Induced Fit Favors Reactivity - Lactate Dehydrogenase (LDH)

• LDH is an example of an enzyme that uses an induced-fit mechanism.
• Dehydrogenases are involved in oxidation-reduction reactions where a hydride (H-) anion is transferred.

Catalytic Mechanisms

• Acid/base catalysis is a common mechanism employed by enzymes.
• Other mechanistic strategies include nucleophilic mechanisms.

Nucleophilic Mechanisms

• Serine and Cysteine residues in enzymes are common nucleophiles in catalytic mechanisms.

Chymotrypsin (Nucleophilic Mechanism Example)

• Chymotrypsin is a protease that preferentially cleaves peptide bonds next to aromatic amino acid residues (F, Y, W).
• Chymotrypsin employs a catalytic triad of Serine, Histidine, and Aspartate.
• A detailed mechanism of Chymotrypsin's reaction was described through the sequential steps of nucleophilic attack on amide, proton transfer, collapse of the intermediate tetrahedral intermediate, ester hydrolysis and product release.

How can we use this information to design inhibitors?

• Inhibitors can be designed to bind to the enzyme active site, disrupting the catalytic mechanism.
• Inhibitors can be designed to trap the serine residue.
• Inhibitors can be designed to bind the His residue.

Allosteric Regulation of Enzymes

• Allosteric inhibitors (or activators) bind to locations on the enzyme (allosteric sites) outside the active site.

• Allosteric inhibitors bind reversibly.

• An induced fit alters the active site of the enzyme and makes the active site less accessible to the substrate.

• Increasing substrate concentration will not reverse the allosteric inhibition.

• Allosteric regulation is common with kinase targets.

• Enzymes exhibiting allosteric regulation are frequently at the start of biosynthetic pathways, where the final product binds to an allosteric site to modulate enzymatic activity.

• Kinases covalently attach phosphate groups to their targets, utilizing ATP as the phosphate source.

Design of MEK1 Inhibitors

• MEK1 inhibitors are non-ATP competitive, and bind to a specific pocket in the protein.
• Specific inhibitors target unique pockets of the protein (MEK1) with high affinity. Key structure examples are included in the presented data.

More Target Binding

• Inhibitors bind to the target protein with high affinity.
• High affinity allows for potent inhibition of the target.
• Mutations in the binding pocket can affect the affinity of the inhibitor for the protein.
• Alanine scanning can be used to determine critical amino acids in the binding pocket responsible for binding.
• Mutating amino acid residues in that determine structure and function can have profound effects on the potency and selectivity of an inhibitor.