Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation

Snake venom of <i>Naja naja</i> comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA₂), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA₂. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA₂ were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca²⁺, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca²⁺ as well as the inflammatory functions of PLA₂. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma

印度眼镜蛇（Naja naja）的蛇毒含有多种酶类，其中水溶性蛋白水解酶、磷脂酶A₂（PLA₂）因其诸多不良反应广受关注，包括细胞毒性、心脏毒性、溶血作用、抗凝作用与降压作用，同时具备极强的神经毒性。由于现有抗蛇毒疗法疗效有限，开发强效PLA₂抑制剂的相关药理学研究受到广泛关注。为此，研究团队基于Glide超高精度对接（Glide extra precision docking）与MM-GBSA重打分函数，对34种经实验验证的多样化PLA₂合成抑制剂进行了初步筛选。随后，对10种潜在命中化合物开展诱导契合对接（induced fit docking）分析，最终筛选出排名前三的潜在抑制剂。研究发现，这三类抑制剂可与钙离子（Ca²⁺）、二硫键结合位点以及磷脂酰胆碱激活位点相结合，由此可能阻断PLA₂的钙离子依赖催化活性及其炎症介导功能。上述化合物在多项理化性质与药理学相关描述符方面均表现优异。研究团队通过密度泛函理论（density functional theory）对所有化合物的能隙与热力学性质进行了分析，以探究其化学反应活性与热力学稳定性。对对接复合物开展时长100纳秒的分子动力学模拟，以评估其结构稳定性与结合模式，并通过MM-PBSA分析计算结合能。综上，本研究筛选得到的化合物有望用于PLA₂的靶向抑制。本文由Ramaswamy H. Sarma提交。