A Combined Crystallographic and Molecular Dynamics Study of Cathepsin L Retrobinding Inhibitors

Abstract

)These authors contributed equally to the work.Received May 7, 2009 We report the crystal structures of three noncovalent retrobinding inhibitors in complex with mature cathepsin L up to resolutions of 2.5, 1.8, and 2.5 Å , respectively. These inhibitors were Bpa-(Nε-Bpa)-Lys-DArg-Tyr-Npe, Bpa-(Nε-Bpa)Lys-DArg-Phe-Npe, and Bpa-MCys-DArg-Phe-Npe, where Bpa = biphenylacetyl and Pea = N-phenylethyl. These were selected to clarify the binding mode of the biphenyl groups in the S 0 subsites because the addition of a second biphenyl does not improve potency. Examination of the symmetry-related monomers in the crystal structures revealed inhibitor-inhibitor crystal packing interactions. Molecular dynamics simulations were then used to explore the structure and dynamical behavior of the isolated protein-ligand complexes in solution. In the simulations, the backbone biphenyl groups for all three inhibitors ended up in the same location despite having started out in different orientations in the initial crystal structure conformations. The lack of improved potency of the larger inhibitors over the smaller one is attributed to a correspondingly greater entropic cost of binding.

A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L

“…The authors further investigated the binding mode of this class of inhibitors by means of co-crystal structure and molecular modeling. This revealed that (a) arginine residue of the inhibitor occupied the S1 pocket, (b) phenyl alanine residue found favorable hydrophobic interactions within the S2 pocket, (c) 2-phenylethyl group pointed toward S3 pocket, (d) the methionine residue showed optimal interaction within S1 pocket, and (e) the biphenyl acetyl group extended to the S3 pocket for favorable interactions [95,128]. This class of inhibitors has shown resistance to enzyme-dependent hydrolysis and demonstrates the reversible mode of enzyme inactivation.…”

Cysteinyl cathepsins and mast cell proteases in the pathogenesis and therapeutics of cardiovascular diseases

“…The field is currently focused on the development of reversible cathepsin inhibitors (Wiener et al, 2010). Few peptide-based CatL inhibitors were found reversibly binding to CatL with high potency (K i = 19~45 nM) and selectivity (64~333-fold), compared with CatL’s inhibitions to CatB or CatK (Table 2) (Chowdhury et al, 2002; Shenoy et al, 2009). The most recent CatL-selective and reversible inhibitors are thiocarbazate derivatives (Table 2).…”

Structural basis for reversible and irreversible inhibition of human cathepsin L by their respective dipeptidyl glyoxal and diazomethylketone inhibitors

“…Cathepsin L in complex with propeptide-mimetic reverse binding non-covalent inhibitors has been extensively studied by us (Chowdhury et al, 2002(Chowdhury et al, , 2008Shenoy et al, 2009). The design of these inhibitors is based on the propeptide region of procathepsin L, which is a potent inhibitor of its mature form.…”