Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes

Novel chemical controls are needed that selectively target human, animal, and plant parasitic nematodes with reduced adverse effects on the host or the environment. We hypothesize that the phosphodiesterase (PDE) enzyme family represents a potential target for development of novel nematicides and anthelmintics. To test this, we identified six PDE families present in the nematode phylum that are orthologous to six of the eleven human PDE families. We characterized the binding interactions of family-selective PDE inhibitors with human and C. elegans PDE4 in conjunction with molecular dynamics (MD) simulations to evaluate differences in binding interactions of these inhibitors within the PDE4 catalytic domain. We observed that roflumilast (human PDE4-selective inhibitor) and zardaverine (selective for human PDE3 and PDE4) were 159- and 77-fold less potent, respectively, in inhibiting C. elegans PDE4. The pan-specific PDE inhibitor isobutyl methyl xanthine (IBMX) had similar affinity for nematode and human PDE4. Of 32 residues within 5 Å of the ligand binding site, five revealed significant differences in non-bonded interaction energies (van der Waals and electrostatic interaction energies) that could account for the differential binding affinities of roflumilast and zardaverine. One site (Phe506 in the human PDE4D3 amino acid sequence corresponding to Tyr253 in C. elegans PDE4) is predicted to alter the binding conformation of roflumilast and zardaverine (but not IBMX) into a less energetically favorable state for the nematode enzyme. The pharmacological differences in sensitivity to PDE4 inhibitors in conjunction with differences in the amino acids comprising the inhibitor binding sites of human and C. elegans PDE4 catalytic domains together support the feasibility of designing the next generation of anthelmintics/nematicides that could selectively bind to nematode PDEs.

亟需开发可选择性靶向人、动物及植物寄生线虫，且对宿主或环境不良反应更低的新型化学防控策略。我们提出假说：磷酸二酯酶（PDE）酶家族可作为开发新型杀线虫剂与抗蠕虫药的潜在靶点。为验证该假说，我们鉴定出线虫门中存在6个与人类11个PDE家族中6个直系同源的PDE家族。我们结合分子动力学（MD）模拟，对家族选择性PDE抑制剂与人类及秀丽隐杆线虫（C. elegans）PDE4的结合相互作用进行了表征，以评估这些抑制剂在PDE4催化结构域内结合相互作用的差异。我们观察到，罗氟司特（人类PDE4选择性抑制剂）与扎达维林（对人类PDE3和PDE4具有选择性）在抑制秀丽隐杆线虫PDE4时，效力分别仅为抑制人类PDE4的1/159和1/77。泛特异性PDE抑制剂异丁基甲基黄嘌呤（IBMX）对线虫与人类PDE4的结合亲和力相近。在配体结合位点5Å范围内的32个氨基酸残基中，有5个残基的非键相互作用能（范德华力与静电相互作用能）存在显著差异，这可解释罗氟司特与扎达维林结合亲和力的差异。其中一个位点（人类PDE4D3氨基酸序列中的Phe506，对应秀丽隐杆线虫PDE4中的Tyr253）被预测会改变罗氟司特和扎达维林（而非IBMX）的结合构象，使其在线虫酶中处于能量上更不利的状态。人类与秀丽隐杆线虫PDE4催化结构域在对PDE4抑制剂的敏感性差异，以及二者抑制剂结合位点的氨基酸组成差异，共同支持了开发可选择性结合线虫PDE的新一代抗蠕虫药/杀线虫剂的可行性。