P1 Glutamine isosteres in the design of inhibitors of 3C/3CL protease of human viruses of the Pisoniviricetes class

Abstract

Viral infections are one of the leading causes of acute morbidity in humans and much endeavour has been made by the synthetic community for the development of drugs to treat associated diseases. Peptide-based enzyme inhibitors, usually short sequences of three or four residues, are one of the classes of compounds currently under development for enhancement of their activity and pharmaceutical properties. This review reports the advances made in the design of inhibitors targeting the family of highly conserved viral proteases 3C/3CL^pro, which play a key role in viral replication and present minimal homology with mammalian proteases. Particular focus is put on the reported development of P₁ glutamine isosteres to generate potent inhibitors mimicking the natural substrate sequence at the site of recognition.'

Fig. 1. (A) Hexapeptide recognition sequence of 3C/3CL^pro, where the scissile bond is located between P₁ (Gln) and P_1′. (B) Typical inhibitor design targeting 3C/3CL^pro.

Fig. 2. Representative 3C/3CL^pro inhibitors possessing a P₁ (l)-glutamine residue with various electrophilic warheads.

Scheme 1. Generalised formation of hemiaminal B via tautomerisation of P₁ glutamine inhibitors A onto the electrophilic warhead.

Fig. 3. Representative examples of P₁N-alkyl-Gln inhibitors targeting 3C/3CL^pro.

Fig. 4. Representative examples of P₁ Met derived inhibitors and their P₁ Gln/N-alkyl-Gln analogues targeting 3C/3CL^pro.

Fig. 5. (A) Inhibitors targeting 3C/3CL^pro containing non-proteogenic P₁ isosteres. (B) Hydrophobic P₁ residue inhibitors targeting 3C/3CL^pro.

Scheme 2. Putative mechanism of reversible covalent inhibition of a cysteine protease by SMAIs.

Fig. 6. Representative examples of P₁ His inhibitors targeting SARS-CoV 3CL^pro.

Fig. 7. Representative examples of P₁ aza-Gln inhibitors targeting 3C/3CL^pro.

Fig. 8. Representative examples of macrocyclic lactam inhibitors containing a P₁ Gln residue.

Fig. 9. (A) Development of HRV inhibitors possessing a P₁ (S)-γ-lactam moiety. (B) Alternative P₁ lactam isosteres.

Fig. 10. Representative examples of inhibitors targeting 3C/3CL^pro containing a P₁ (S)-γ/δ-lactam isostere.

Fig. 11. Representative examples of SARS-CoV-2 inhibitors in preclinical (A) or clinical (B) development.

Scheme 3. (A) The primary route of metabolism of nirmatrelvir 51via CYP3A4 hydroxylation of the P₁ (S)-γ-lactam moiety. (B) Minor metabolites products of nirmatrelvir 51via CYP3A4 hydroxylation of the P₂ and P₃ moiety.