Ramakrishnan Chandrasekaran, Joshi Vikram, Joseph Joseph Mavelithuruthel, Vishwanath Bannikuppe S, Velmurugan Devadasan
Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai, 600025, India.
Chem Biol Drug Des. 2014 Oct;84(4):379-92. doi: 10.1111/cbdd.12332. Epub 2014 Jun 3.
Crystal structures available for Daboia russelli venom PLA(2) confirm that it undergoes dimerization with asymmetry and hence difference in the conformation of active site of the two subunits. The active site of subunit A is open and that of subunit B is closed. Pharmacophore models were generated based on the interaction of different types of inhibitors with their preferred subsites in the active site of subunit A. Particularly, the features responsible for recognizing subsites 1-3 and those of subsites 4-6 were combined as these two are involving in inflammation and anticoagulation processes, respectively. Pharmacophore model was edited to make the geometry suitable for the active site of both the subunits A and B. Final model is validated and subjected for screening a library of druglike compounds. Eight compounds were shortlisted and subjected for molecular docking and dynamics simulation to assess their binding mode with both the subunits. Based on the hydrophobic interactions and binding free energy, four compounds were selected for further biochemical assay. The overall results suggest that two compounds can bind both the subunits of PLA(2) of Daboia russelli venom in spite of its aggregated form and other two inhibit structurally very similar Naja naja PLA(2).
已获得的锯鳞蝰蛇毒磷脂酶A2（PLA(2)）的晶体结构证实，它会发生不对称二聚化，因此两个亚基活性位点的构象存在差异。亚基A的活性位点是开放的，亚基B的活性位点是封闭的。基于不同类型抑制剂与其在亚基A活性位点中偏好亚位点的相互作用生成了药效团模型。特别地，负责识别亚位点1 - 3的特征和亚位点4 - 6的特征被组合在一起，因为这两者分别涉及炎症和抗凝过程。对药效团模型进行编辑，使其几何形状适合亚基A和B的活性位点。对最终模型进行验证，并用于筛选类药物化合物库。筛选出八种化合物，并对其进行分子对接和动力学模拟，以评估它们与两个亚基的结合模式。基于疏水相互作用和结合自由能，选择四种化合物进行进一步的生化分析。总体结果表明，尽管锯鳞蝰蛇毒PLA(2)呈聚集形式，但仍有两种化合物可以与它的两个亚基结合，另外两种化合物则抑制结构非常相似的眼镜蛇PLA(2)。
