Recent advances in the development of covalent inhibitors

Abstract

The use of covalent inhibitors in the field of drug discovery has attracted considerable attention in the 2000s. As a result, more than 50 covalent drugs are currently on the market, and numerous covalent drug candidates are now under development. Therefore, interest in covalent drugs is expected to continue in the future. The purpose of this focused review is to provide an understanding of the development of covalent inhibitors by describing their inherent characteristics, possibilities, and limitations based on their mechanistic differences from noncovalent inhibitors. We also introduce the latest covalent warheads that can be applied to the development of potential covalent inhibitors.

Fig. 1. General mechanism underlying the action of (a) irreversible covalent inhibitors and (b) reversible covalent inhibitors.

Fig. 2. Hypothetical pharmacokinetic (PK)/pharmacodynamic (PD) profiles of noncovalent and covalent inhibitors with the same PK parameters.

Fig. 3. α,β-Unsaturated carbonyl moiety acrylamide as cysteine-targeting covalent warheads. (a) Chemical structure of acrylamide. (b) Mechanism of acrylamide forming a covalent adduct with cysteine. (c) Chemical structure and year of approval of acrylamide-based FDA-approved drugs neratinib, dacomitinib, zanubrutinib.

Fig. 4. α,β-Unsaturated carbonyl moiety cyanoacrylamide as cysteine-targeting covalent warheads. (a) Chemical structure of cyanoacrylamide. (b) Mechanism of cyanoacrylamide forming a reversible covalent adduct with cysteine. (c) Chemical structure of a cyanoacrylamide-based reversible covalent BTK inhibitor and PPARγ. (d) X-ray crystal structure of cyanoacrylamide-based reversible covalent inhibitor bound to Cys481 in BTK (PDB code: 4YHF) and bound to Cys285 in PPARγ (PDB code: 6IJR).

Fig. 5. α,β-Unsaturated carbonyl moiety allenamide as cysteine-targeting covalent warheads. (a) Chemical structure of allenamide. (b) Mechanism of allenamide forming a covalent adduct with cysteine. (c) Chemical structure of allenamide-based irreversible covalent EGFR inhibitor.

Fig. 6. Sulfur(vi) warheads used in IDD approaches. (a) Chemical structure of aryl fluorosulfate and sulfuramidimidoyl fluorides. (b) Mechanism of aryl fluorosulfate and sulfuramidimidoyl fluorides forming covalent adduct with tyrosine. (c) Chemical structure of an aryl fluorosulfate probe and sulfuramidimidoyl fluoride probe which is an irreversible covalent PARP1 inhibitor discovered by the IDD approach.

Fig. 7. Heteroaromatic sulfones reported as thiol-reactive electrophiles. (a) Chemical structure of 2-sulfonylpyridine. (b) Mechanism of 2-sulfonylpyridine forming a covalent adduct with cysteine. (c) Chemical structure of 2-sulfonylpyridine-based irreversible covalent ADA modifier.

Fig. 8. Alkynyl benzoxazine and dihydroquinazoline reported as cysteine-targeting warheads. (a) Chemical structure of alkynyl benzoxazine and dihydroquinazoline. (b) Mechanism of alkynyl benzoxazine and dihydroquinazoline forming covalent adduct with cysteine. (c) Chemical structure of alkynyl benzoxazine-based JAK3 and c-KIT covalent inhibitor (d) X-ray crystal structure of c-KIT covalent inhibitor bound to Cys788 in c-KIT (PDB code: 6XVB).

Fig. 9. Strain-released motif of BCB amide reported as a warhead of cysteine-targeting covalent inhibitor. (a) Chemical structure of the BCB amide. (b) Mechanism of the BCB amide forming a covalent adduct with cysteine. (c) Chemical structure of the BCB amide-based irreversible covalent BTK inhibitor.

Fig. 10. Strain-released motif aziridine reported as a warhead of cysteine-targeting covalent inhibitor. (a) Chemical structure of aziridine. (b) Mechanism of aziridine forming covalent adduct with cysteine. (c) Chemical structure of aziridine-based irreversible covalent NSD1 inhibitor.

Fig. 11. Terminal alkyne moieties reported as cysteine-targeting warheads. (a) Chemical structure of the terminal alkyne moiety. (b) Mechanism of the terminal alkyne moiety forming a covalent adduct with cysteine. (c) Chemical structure of the terminal alkyne moiety-based CatK covalent inhibitor. (d) X-ray crystal structure of the CatK covalent inhibitor bound to Cys25 in CatK (PDB code: 6QBS).