Bassani Davide, Pavan Matteo, Sturlese Mattia, Moro Stefano
Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy.
Pharmaceuticals (Basel). 2022 Mar 11;15(3):346. doi: 10.3390/ph15030346.
The function of the allosteric sodium ion in stabilizing the inactive form of GPCRs has been extensively described in the past decades. Its presence has been reported to be essential for the binding of antagonist molecules in the orthosteric site of these very important therapeutical targets. Among the GPCR-antagonist crystal structures available, in most cases, the sodium ion could not be experimentally resolved, obliging computational scientists using GPCRs as targets for virtual screening to ask: "Should the sodium ion affect the accuracy of pose prediction in docking GPCR antagonists?" In the present study, we examined the performance of three orthogonal docking programs in the self-docking of GPCR antagonists to try to answer this question. The results of the present work highlight that if the sodium ion is resolved in the crystal structure used as the target, it should also be taken into account during the docking calculations. If the crystallographic studies were not able to resolve the sodium ion then no advantage would be obtained if this is manually inserted in the virtual target. The outcomes of the present analysis are useful for researchers exploiting molecular docking-based virtual screening to efficiently identify novel GPCR antagonists.
在过去几十年里，变构钠离子在稳定G蛋白偶联受体（GPCR）无活性形式方面的作用已被广泛描述。据报道，钠离子的存在对于这些非常重要的治疗靶点的正构位点中拮抗剂分子的结合至关重要。在现有的GPCR-拮抗剂晶体结构中，在大多数情况下，钠离子无法通过实验解析出来，这使得将GPCR作为虚拟筛选靶点的计算科学家不禁要问：“钠离子会影响对接GPCR拮抗剂时构象预测的准确性吗？”在本研究中，我们研究了三种正交对接程序在GPCR拮抗剂自对接中的性能，试图回答这个问题。目前这项工作的结果突出表明，如果在用作靶点的晶体结构中解析出了钠离子，那么在对接计算过程中也应予以考虑。如果晶体学研究未能解析出钠离子，那么手动将其插入虚拟靶点将不会带来任何优势。本分析结果对于利用基于分子对接的虚拟筛选来有效鉴定新型GPCR拮抗剂的研究人员很有用。
