Peptidomimetic

Class B peptidomimetics

This class of peptidomimetics encompasses peptides with a large number of non-natural amino acids, major backbone modifications or larger non-natural building fragments that resemble the conformation of a particular peptide binding motif. Examples involve D-peptide and peptidic foldamers such as beta-peptides.

Class C peptidomimetics

These structural mimetics include molecules that are highly modified when compared to their parent peptide sequence. Usually, a small-molecular scaffold is appyled to project groups in analogy to the bioactive conformation of a peptide.

Class D peptidomimetics

These mechanistic mimetics do not directly recapitulate the side chains or conformation of a peptide but mimic its mode-of-action. Class D peptidomimetics can be directly designed from a small peptide sequence or identified the screening of compound libraries. For example, Nirmatrelvir is an orally-active small molecule drug derived from lufotrelvir, a modified L-peptide.

Uses and examples

The use of peptides as drugs has some disadvantages because of their bioavailability and biostability. Rapid degradation, poor oral availability, difficult transportation through cell membranes, nonselective receptor binding, and challenging multistep preparation are the major limitations of peptides as active pharmaceutical ingredients. Therefore, small protein-like chains called peptidomimetics could be designed and used to mimic native analogs and conceivably exhibit better pharmacological properties. Many peptidomimetics are utilized as FDA-approved drugs, such as Romidepsin (Istodax), Atazanavir (Reyataz), Saquinavir (Invirase), Oktreotid (Sandostatin), Lanreotide (Somatuline), Plecanatide (Trulance), Ximelagatran (Exanta), Etelcalcetide (Parsabiv), and Bortezomib (Velcade).

Peptidomimetic approaches have been utilized to design small molecules that selectively target cancer cells, an approach known as targeted chemotherapy, by inducing programmed cell death by a process called apoptosis. The following two examples mimic proteins involved in key Protein–protein interactions that reactivate the apoptotic pathway in cancer but do so by distinct mechanisms.

In 2004, Walensky and co-workers reported a stabilized alpha helical peptide that mimics pro-apoptotic BH3-only proteins, such as BID and BAD. This molecule was designed to stabilize the native helical structure by forming a macrocycle between side chains that are not involved in binding. This process, referred to as peptide stapling, uses non-natural amino acids to facilitate macrocyclization by ring-closing olefin metathesis. In this case, a stapled BH3 helix was identified which specifically activates the mitochondrial apoptotic pathway by antagonizing the sequestration of BH3-only proteins by anti-apoptotic proteins (e.g. Bcl-2, see also intrinsic and extrinsic inducers of the apoptosis). This molecule suppressed growth of human leukemia in a mouse xenograft model.

Also in 2004, Harran and co-workers reported a dimeric small molecule that mimics the proapoptotic protein Smac (see mitochondrial regulation in apoptosis). This molecule mimics the N-terminal linear motif Ala-Val-Pro-Ile. Uniquely, the dimeric structure of this peptidomimetic led to a marked increase in activity over an analogous monomer. This binding cooperativity results from the molecule's ability to also mimic the homodimeric structure of Smac, which is functionally important for reactivating caspases. Smac mimetics of this type can sensitize an array of non-small-cell lung cancer cells to conventional chemotherapeutics (e.g. Gemcitabine, Vinorelbine) both in vitro and in mouse xenograft models.

Heterocycles are often used to mimic the amide bond of peptides. Thiazoles, for example, are found in naturally occurring peptides and used by researchers to mimic the amide bond of peptides.