ANS 24- Design of drugs to interact with enzymes 1

What are enzymes?

• Endogenous proteins that catalytically affect chemical transformations

• Specificity is tailored to requirements

• Turnover rates can be enormous

• Classified into six mechanistic categories

What are proteases?

• Hydrolytically cleave peptide amide bonds- difficult to break, so need enzymes

• Four mechanistic classes:

Serine Protease Ser-CH2-OH 7

Zn (Metallo)protease H2O 7

Aspartic H2O 3 - 6

Cystein (Thiol). Cys-CH2-SH 7

What is the terminology for enzyme binding pockets?

• determine binding to substrate amino side chains

• Prime is used for residues closer to the C-terminus of the peptide chain

• c terminus- near carboxylic acid - p1” near it

• p1 on the other side of the bond to be cleaved

• The bond is usually an amide bond

What is aspartic protease ?

• complex active site - all have two catalytic sites. active asp residues

• enzyme cleaves the scissile peptide bond in the substrate

What is the Aspartic acid proteases reaction?

• general acid-base catalysis- no covalent intermediates - no bonds forming

• aspartate residues are in different protonation states during catalysis

• nucleophile = water

What is the design for aspartic proteases inhibitors?

• A non-hydrolysable dipeptide isostere can be used for the replacement of the scissile bond

• Pauling’s Principle: Enzyme-substrate interaction is strongest at this transition state, making it the
  ideal target for inhibitor mimicry

Note - when designing a mimic structure to this transition state = resistant to hydrolysis

• hydroxyl group important = mimics the tetrahedral intermediate

Describe the aspartic proteases inhibitor binding?

criteria in consideration:
• Active Site Coordination: The hydroxyl group of the inhibitor’s isostere forms critical, strong hydrogen bonds with the catalytic carboxyl groups of Aspartic acid.
• Replacing Water: This hydroxyl group effectively displaces the catalytic water molecule found in the native enzyme's active site.
• Subsite Binding: Inhibitors are optimised by incorporating specific ligands that fit into the enzyme's
S1, S1', S2, and S2’ subsites to achieve high potency and selectivity