Quantum Mechanics/Molecular Mechanics Study on Caspase-2 Recognition by Peptide Inhibitors

摘要

For a variety of biological and medical reasons, the ongoing development of humane caspase-2 inhibitors is of vital importance. Herein, a hybrid (Quantum Mechanics/Molecular Mechanics - QM/MM), two-layered molecular model is derived in order to understand better the affinity and specificity of peptide inhibitor interaction with caspase-2. By taking care of both the unique structural features and the catalytic activity of human caspase-2, the critical enzyme residues (E217, R378, N379, T380, and Y420) with the peptide inhibitor are treated at QM level (the Self-Consistent-Charge Density-Functional Tight-Binding method with the Dispersion correction (SCC-DFTB-D)), while the remaining part of the complex is treated at MM level (AMBER force field). The QM/MM binding free energies (BFEs) are well-correlated with the experimental observations and indicate that caspase-2 uniquely prefers a penta-peptide such as VDVAD. The sequence of VDVAD is varied in a systematic fashion by considering the physicochemical properties of every constitutive amino acid and its substituent, and the corresponding BFE with the inhibition constant (K-i) is evaluated. The values of K-i for several caspase-2:peptide complexes are found to be within the experimental range (between 0.01 nM and 1 1 mu M). The affinity order is: VELAD (K-i = 0.081 nM) > VDVAD (K-i = 0.23 nM) > VEIAD (K-i = 0.61 nM) > VEVAD (K-i = 3.7 nM) > VDIAD (K-i = 4.5 nM) etc. An approximate condition needed to be satisfied by the kinetic parameters (the Michaelis constant - K-M and the specificity constant - k(cal)/K-M) for competitive inhibition is reported. The estimated values of k(cal)/K-M, being within the experimentally established range (between 10(-4) and 10(-1) mu M (1 )s(-1)), indicate that VELAD and VDVAD are most specific to caspase-2. These two particular peptides are nearly 1.5, 3 and 4 times more specific to the receptor than VEIAD, VEVAD and VDIAD respectively. Additional kinetic threshold, aimed to discriminate tightly bound inhibitors, is given.