Amino acids and drug target interactions

Amino acid general structure

Contains amine, carboxyl group, and side chain (R group).

N‑terminus

Left end of peptide chain.

C‑terminus

Right end of peptide chain.

Amino acid stereochemistry

Almost always S‑configuration.

Alkyl amino acids

Gly, Ala, Val, Leu, Ile, Pro.

Polar amino acids

Ser, Thr, Asn, Gln.

Sulfur‑containing amino acids

Cys, Met.

Aromatic amino acids

Phe, Tyr, Trp.

Anionic amino acids

Asp, Glu.

Cationic amino acids

Lys, Arg, His.

Hydrogen bond donor (HBD)

Atom that donates hydrogen in H‑bond.

Hydrogen bond acceptor (HBA)

Atom with lone pair accepting H‑bond.

Electrostatic interactions

Attraction between charged groups.

Hydrogen bond ideal geometry

Linear, 2.5–3.5 Å.

Aromatic interactions

π‑π stacking or edge‑to‑face interactions.

Cation‑π interaction

Attraction between cation and aromatic ring.

Hydrophobic interactions

Non‑polar groups clustering away from water.

Sildenafil mechanism

PDE5 inhibitor increasing cGMP → smooth muscle relaxation.