Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements

Area of Science:

• Medicinal Chemistry
• Structural Biology
• Enzymology

Background:

• Cathepsin S (CatS) is a cysteine protease implicated in various diseases.
• Previous pyrazole-based inhibitors showed promise but required further structural understanding for optimization.
• Elucidating the binding mode is crucial for designing more potent and selective inhibitors.

Purpose of the Study:

• To determine the binding mode of pyrazole-based CatS inhibitors using X-ray crystallography.
• To facilitate the design and synthesis of novel, potent CatS inhibitors.
• To characterize the structural basis for the activity of new arylalkyne analogs.

Main Methods:

• X-ray crystallography of a Cys25Ser mutant of cathepsin S bound to inhibitor 1.
• Structure-based drug design of arylalkyne analogs.
• Enzyme inhibition assays to determine IC50 values.
• X-ray crystallography of a potent arylalkyne inhibitor (32) bound to CatS.

Main Results:

• The crystal structure of inhibitor 1 elucidated the binding mode of pyrazole-based CatS inhibitors.
• A new class of arylalkyne analogs was designed and synthesized.
• Optimized analogs demonstrated potent CatS inhibition with IC50 values ranging from 40-300 nM.
• X-ray structure of analog 32 confirmed the binding of the arylalkyne moiety within the S1 pocket of CatS.

Conclusions:

• Structural insights into CatS inhibitor binding enabled the rational design of potent analogs.
• Arylalkyne analogs represent a promising new class of CatS inhibitors.
• The S1 pocket is a key binding site for these novel inhibitors, guiding future drug development efforts.