The cathepsins constitute an 11-member family of proteases involved in protein degradation. Cathepsin S is highly expressed in antigen-presenting cells, where it degrades major histocompatiability complex class II (MHC II)-associated invariant chain. CatS is a candidate target for regulating immune hyper-responsiveness, as the inhibition of CatS may limit antigen presentation. [1-3].

Cathepsin S

The cathepsins constitute an 11-member family of proteases involved in protein degradation. Cathepsin S is highly expressed in antigen-presenting cells, where it degrades major histocompatiability complex class II (MHC II)-associated invariant chain. CatS is a candidate target for regulating immune hyper-responsiveness, as the inhibition of CatS may limit antigen presentation. [1-3].

This data set comprises non-peptidic, non-covalent, small molecule inhibitors across a three order of magnitude range (nM to μM) of IC50s for CatS. Specifically, we provide 136 CatS inhibitors for affinity prediction, 24 for pose prediction, and 33 for free energy prediction.

Binding pocket information

The conformation of the CatS binding pocket can change, depending on the nature of the bound ligand. In particular, Phe211 in the S2 pocket adopts a different conformation, depending on the size of the P2 moiety of the ligand [4]. If the P2 moiety is small, Phe211 swings into a conformation that closes the entrance to the deeper part of the S2 pocket. However, a larger P2 moiety can induce Phe211 to swing open, allowing for ligand binding to the deeper portion of the S2 pocket [5].

For details of the binding assays, we were referred to publications from the Janssen group, which describe the following binding assays conditions [6]:

"In general, the assays were run using fluorescence resonance energy transfer-based substrates. For example, the cathepsin S, L, and L2 assays used the substrate (Aedens)EK ARVLAEAA(Dabcyl)K-amide and cathepsin S cleaves between amino acids Leu-6 and Ala-7. The fluorescence of the aedens group is quenched by the dabcyl moiety in the intact peptide. Upon cleavage by cathepsin S, the quenching is released and the fluorescence of the aedens group can be measured.

The cysteine CatS assays were run in 100-μl volume with a buffer consisting of 100 mM sodium acetate, pH 5.0, containing 100 mM NaCl and 1 mM dithiothreitol, except for cathepsin Z, which used 10 mM dithiothreitol and cathepsins E, D, and napsin where no dithiothreitol was present. The enzymes were mixed with 7.5 ml of buffer and then 75 μl was added to a Dynax black Mi- crofluor 2 plate. To this, 5 μl of a 20 μl solution of compound in 30% DMSO was added. This was followed by the addition of 20 μl of 5X substrate to initiate the reaction. In all cases, an 11 point 1:2 dilution of the compound was used at seven substrate concentrations (also 1:2). The increase in fluorescence was measured on a Cytofluor II (Applied Biosystems, Foster City, CA) with an excitation filter of 360/40 nm and an emission filter of 460/40 nm. A reading was made every minute for 20 to 60 min, depending on the assay, and the slope obtained from a linear regression of this time course was used as the reaction rate."

The structure files provided by Janssen, did not specify crystallization conditions. However, manuscripts provided to us that discuss PDB IDs 3iej, 3mpe, and 3kwn, list the following [1-3]:

"Crystallization conditions: 100MM sodium acetate, pH 4.5, 200mm ammonium acetate, 25% PEG 8000. Protein concentration 7 mg/ml, vapor diffusion, sitting drop, temperature 293 K."

1. Ameriks MK, Bembenek SD, Burdett MT, et al (2010) Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors. Bioorg Med Chem Lett 20:4060-4064. doi: 10.1016/j.bmcl.2010.05.086

2. Wiener DK, Lee-Dutra A, Bembenek S, et al (2010) Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors. Bioorg Med Chem Lett 20:2379-2382. doi: 10.1016/j.bmcl.2010.01.103

3. Ameriks MK, Axe FU, Bembenek SD, et al (2009) Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements. Bioorg Med Chem Lett 19:6131-6134. doi: 10.1016/j.bmcl.2009.09.014

4. Pauly TA, Sulea T, Ammirati M, et al (2003) Specificity Determinants of Human Cathepsin S Revealed by Crystal Structures of Complexes,. Biochemistry (Mosc) 42:3203-3213. doi: 10.1021/bi027308i

5. Markt P, McGoohan C, Walker B, et al (2008) Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening. J Chem Inf Model 48:1693-1705. doi: 10.1021/ci800101j

6. Thurmond RL, Sun S, Sehon CA, et al (2004) Identification of a Potent and Selective Noncovalent Cathepsin S Inhibitor. J Pharmacol Exp Ther 308:268-276. doi: 10.1124/jpet.103.056879