Arya Praffulla Kumar, Mandal Pranabesh, Barik Krishnendu, Singh Durg Vijay, Kumar Anil
Department of Bioinformatics, Central University of South Bihar, Gaya, India.
J Biomol Struct Dyn. 2024 Oct;42(16):8293-8306. doi: 10.1080/07391102.2023.2256865. Epub 2023 Sep 11.
DNA topoisomerase I (Topo I) is a ubiquitous enzyme that plays a crucial role in resolving the topological constraints of supercoiled DNA during various cellular activities, including repair, replication, recombination, transcription, and chromatin remodeling. Multiple studies have confirmed the essential role of Topo I in nucleic acid metabolism of , the kinetoplastid parasite responsible for visceral leishmaniasis or kala-azar. Inhibition of this enzyme has shown promise as a strategy for therapy against visceral leishmaniasis. However, current treatment options suffer from limitations related to effectiveness, cost, and side effects. To address these challenges, computational methods have been employed in this study to investigate the inhibition of DNA topoisomerase I (LdTopo I) by phytochemicals derived from Indian medicinal plants known for their anti-leishmanial activity. A library of phytochemicals and known inhibitors was assembled, and virtual screening based on docking binding affinities was conducted to identify potent phytochemical inhibitors. To assess the drug-likeness of the docked phytochemicals, their physicochemical properties were predicted. Additionally, molecular dynamics (MD) simulations were performed on the docked complexes for a duration of 100 ns to evaluate their stability, intermolecular interactions, and dynamic behavior. Among all the docked phytochemicals, three compounds, namely CID23266147 (withanolide N), CID5488537 (fagopyrine), and CID100947536 (isozeylanone), exhibited the highest inhibitory potential against LdTopo I. These findings hold promise for the development of novel inhibitors targeting LdTopo I, which could potentially lead to improved therapies for visceral leishmaniasis.Communicated by Ramaswamy H. Sarma.
DNA拓扑异构酶I(Topo I)是一种普遍存在的酶,在包括修复、复制、重组、转录和染色质重塑在内的各种细胞活动中,对解决超螺旋DNA的拓扑限制起着关键作用。多项研究证实了Topo I在导致内脏利什曼病或黑热病的动基体寄生虫的核酸代谢中的重要作用。抑制这种酶已显示出作为治疗内脏利什曼病的一种策略的前景。然而,目前的治疗选择存在与有效性、成本和副作用相关的局限性。为了应对这些挑战,本研究采用计算方法来研究具有抗利什曼活性的印度药用植物衍生的植物化学物质对DNA拓扑异构酶I(LdTopo I)的抑制作用。组装了一个植物化学物质和已知抑制剂的文库,并基于对接结合亲和力进行虚拟筛选,以鉴定有效的植物化学抑制剂。为了评估对接的植物化学物质的类药性,预测了它们的物理化学性质。此外,对对接复合物进行了100纳秒的分子动力学(MD)模拟,以评估它们的稳定性、分子间相互作用和动态行为。在所有对接的植物化学物质中,三种化合物,即CID23266147(withanolide N)、CID5488537(原阿片碱)和CID100947536(异泽兰酮),对LdTopo I表现出最高的抑制潜力。这些发现为开发针对LdTopo I的新型抑制剂带来了希望,这可能会导致内脏利什曼病治疗方法的改进。由Ramaswamy H. Sarma传达。