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Almost no peptide of pharmacological interest is an untouched natural sequence. Between the endogenous peptide and the analog being studied there is a set of chemical modifications with a specific purpose: resisting enzymes, locking in the active conformation or changing the pharmacokinetics.
Chain ends
- C-terminal amidation (–CONH₂). It removes the negative charge of the terminal carboxyl and protects against carboxypeptidases. Many natural peptide hormones (oxytocin, vasopressin, calcitonin) are amides; removing the amide usually reduces their activity drastically.
- N-terminal acetylation (Ac–). It neutralizes the charge of the terminal amino group and blocks aminopeptidases. TB-500 (Ac-LKKTETQ) is a direct example.
Conformational constraints
- Disulfide bridges. Two oxidized cysteines form a covalent S–S bond that locks a loop. Oxytocin is cyclic through a disulfide between Cys1 and Cys6.
- Head-to-tail or side-chain cyclization. It reduces flexibility, which usually increases affinity and stability. Melanotan-2 and PT-141 are heptapeptides cyclized through a lactam bridge.
- Stapled peptides. A hydrocarbon bridge between two residues stabilizes an α-helix. It is a design strategy for intracellular targets.
Non-natural amino acids
- D-amino acids. Replacing an L residue with its D enantiomer at a cleavage site prevents enzymatic recognition. SS-31 starts with D-Arg.
- α-Methylated or non-proteinogenic amino acids (Aib, Dmt, Nle). Aib at position 2 protects against DPP-4 cleavage in several GLP-1 analogs (including semaglutide); norleucine replaces methionine to prevent its oxidation.
When you read a sequence with symbols such as Ac-, -NH₂, D-, Aib or a cyclization subscript, they are not decorations: each one explains why that analog lasts longer, degrades less or binds better than the natural peptide it comes from.
Analytical consequence
Each modification changes the theoretical molecular mass. A mass spectrometry COA must match the mass of the modified analog, not that of the natural sequence: a C-terminal amide, for example, reduces the mass by ~1 Da relative to the free acid, and that difference is detectable.
Catalogue compounds mentioned in this lesson
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