Acta Chim Slov. 2020 Sep;67(3):876-884.
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 (Ki) is evaluated. The values of Ki for several caspase-2:peptide complexes are found to be within the experimental range (between 0.01 nM and 1 ?M). The affinity order is: VELAD (Ki=0.081 nM) > VDVAD (Ki=0.23 nM) > VEIAD (Ki=0.61 nM) > VEVAD (Ki=3.7 nM) > VDIAD (Ki=4.5 nM) etc. An approximate condition needed to be satisfied by the kinetic parameters (the Michaelis constant - KM and the specificity constant - kcat/KM) for competitive inhibition is reported. The estimated values of kcat/KM, being within the experimentally established range (between 10-4 and 10-1 ?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.
出于多种生物学和医学原因，持续开发人类胱天蛋白酶-2 抑制剂至关重要。在此，为了更好地理解肽抑制剂与 caspase-2 相互作用的亲和力和特异性，我们推导了一个混合（量子力学/分子力学 - QM/MM）双层分子模型。通过兼顾人类 caspase-2 的独特结构特征和催化活性，用 QM 水平（带有色散校正的自洽电荷密度泛函紧束缚方法（SCC-DFTB-D））处理与肽抑制剂相互作用的关键酶残基（E217、R378、N379、T380 和 Y420），而复合物的其余部分则用 MM 水平（AMBER 力场）处理。QM/MM 结合自由能（BFEs）与实验观察结果很好地相关，并表明 caspase-2 独特地偏爱五肽，例如 VDVAD。通过系统地考虑每个组成氨基酸及其取代基的物理化学性质来改变 VDVAD 的序列，并评估相应的抑制常数（Ki）的 BFE。发现几种 caspase-2：肽复合物的 Ki 值在实验范围内（0.01 nM 至 1 μM 之间）。亲和力顺序为：VELAD（Ki=0.081 nM）>VDVAD（Ki=0.23 nM）>VEIAD（Ki=0.61 nM）>VEVAD（Ki=3.7 nM）>VDIAD（Ki=4.5 nM）等。报告了满足竞争抑制动力学参数（米氏常数 - KM 和特异性常数 - kcat/KM）所需的近似条件。估计的 kcat/KM 值在实验确定的范围内（0.01 nM 至 1 μM 之间），表明 VELAD 和 VDVAD 对 caspase-2 最特异。这两个特定的肽对受体的特异性分别比 VEIAD、VEVAD 和 VDIAD 高 1.5、3 和 4 倍。给出了旨在区分紧密结合抑制剂的额外动力学阈值。
