Chepsiror Curtis, Veldman Wayde, Olotu Fisayo, Tastan Bishop Özlem
Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa.
PLoS One. 2025 May 14;20(5):e0321444. doi: 10.1371/journal.pone.0321444. eCollection 2025.
Targeting Plasmodium falciparum (Pf) aminoacyl tRNA synthetases is a viable strategy to overcome malaria parasite multi-drug resistance. Here, we focused on Pf Isoleucyl tRNA synthetase (PfIleRS) to identify potential allosteric inhibitors from 1019 South African Natural Compounds (SANC). Eleven potential hits, which passed ADMET and PAINS, were selected based on their docking binding affinity which was higher for PfIleRS than for human IleRS. Molecular dynamics simulations revealed that the compounds, particularly SANC456, commonly induced considerable changes in the global conformation and dynamics of PfIleRS, suggesting potential allosteric modulatory effects. Importantly, all 11 SANC hits reduced the binding affinity of the nucleotide AMP molecule by at least 25%. Some SANC ligand-bound systems (SANC456, SANC1095, and SANC1104) significantly increased the distance between the AMP and Ile ligands. Possible explanations for these changes were explored using three dynamic residue network centrality metrics. Betweenness centrality identified a major allosteric pathway in holo PfIleRS spanning the entire protein length. In contrast, SANC382, SANC456, SANC522, SANC806 and SANC1095 ligand-bound systems exhibited delta BC pathways (SANC-protein minus holo-protein), induced by the ligands, extending from their respective pockets into the active site. Additionally, eigenvector centrality revealed two important residue clusters either side of the holo active site which became altered in the ligand-bound systems, indicating possible allosteric activity. Lastly, many SANC systems showed decreased closeness centrality of zinc finger and active site residues, including the HYGH and KMSKR motifs. We believe that the compounds identified in this study as potential allosteric inhibitors have strong translational potential and warrant further investigation through in vitro and in vivo experiments. Overall, they hold promise as starting points for the development of new and effective antimalarial therapies, particularly against multidrug-resistant Plasmodium parasites.
靶向恶性疟原虫（Pf）氨酰基tRNA合成酶是克服疟原虫多重耐药性的一种可行策略。在此，我们聚焦于Pf异亮氨酰tRNA合成酶（PfIleRS），从1019种南非天然化合物（SANC）中筛选潜在的变构抑制剂。基于它们与PfIleRS的对接结合亲和力高于人IleRS，筛选出了11种通过ADMET和PAINS筛选的潜在活性化合物。分子动力学模拟表明，这些化合物，尤其是SANC456，通常会引起PfIleRS整体构象和动力学的显著变化，提示潜在的变构调节作用。重要的是，所有11种SANC活性化合物均使核苷酸AMP分子的结合亲和力降低了至少25%。一些SANC配体结合系统（SANC456、SANC1095和SANC1104）显著增加了AMP与异亮氨酸配体之间的距离。使用三种动态残基网络中心性指标探究了这些变化的可能原因。中介中心性确定了全酶PfIleRS中一条贯穿整个蛋白质长度的主要变构途径。相比之下，SANC382、SANC456、SANC522、SANC806和SANC1095配体结合系统表现出由配体诱导的δBC途径（SANC-蛋白质减去全酶-蛋白质），从各自的口袋延伸至活性位点。此外，特征向量中心性揭示了全酶活性位点两侧的两个重要残基簇，在配体结合系统中发生了改变，表明可能存在变构活性。最后，许多SANC系统显示锌指和活性位点残基（包括HYGH和KMSKR基序）的紧密中心性降低。我们认为，本研究中鉴定出的作为潜在变构抑制剂的化合物具有很强的转化潜力，值得通过体外和体内实验进一步研究。总体而言，它们有望成为开发新型有效抗疟疗法的起点，尤其是针对多重耐药疟原虫。
