Caspases are a family of cysteine proteases that play essential roles in apoptosis (programmed cell death), necrosis, and inflammation. All caspases share a number of distinct features. These include the catalytic triad residues, consisting of the active site Cys285, which is a part of the conserved QACXG pentapeptide sequence, His237 and the backbone carbonyl of residue 177 (caspase-1 numbering). A striking feature of the caspase family is its specificity for substrate cleavage after an Asp residue, which is unique among mammalian proteases.
Increased levels of apoptosis and caspase activity are frequently observed at sites of cellular damage in both acute (myocardial infarction, stroke, sepsis) and chronic (Alzheimer's, Parkinson's and Huntington's Disease) indications. Thus, inhibition of caspase activity with the aim of reducing cell death, and hence, tissue damage, is predicted to be therapeutically beneficial.
To identify potential inhibitors for a number of caspases we used TopomerSearch (SYBYLX), a ligand-based virtual screening tool. For this purpose, as a template, we selected potent caspase inhibitors that were co-crystallized with corresponding proteins. The query features were created based on crystallographic conformations of the ligands. Thereafter, the TopomerSearch was launched for a preselected set of Life Chemicals screening compounds. Finally, compounds with unwanted structures were filtered off using the PAINS filters.
The total number of compounds selected for the Caspase Targeted Library is 2,800.
The following targets and corresponding PDB entries were used for the Library preparation:
- CASP1 (PDB ID: 1RWX)
- CASP2 (PDB ID: 1PYO)
- CASP3 (PDB IDs: 2CNO and 2CNL)
- CASP6 (PDB ID: 3OD5)
- CASP7 (PDB IDs: 3EDR and 2QL9)
- CASP8 (PDB IDs: 1QTN and 3KJN)
- CASP9 (PDB ID: 1NW9)
- Paracaspase (PDB ID: 3V4O)