Doiphode Sayali, Lokhande Kiran Bharat, Ghosh Payel, Swamy K V, Nagar Shuchi
Bioinformatics Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India.
Bioinformatics Centre, Savitribai Phule Pune University, Pune, India.
J Biomol Struct Dyn. 2023 Oct-Nov;41(17):8571-8586. doi: 10.1080/07391102.2022.2135599. Epub 2022 Oct 25.
In a number of human cancers, both cycloxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) are up-regulated and co-expressed, promoting cancer cell proliferation and angiogenesis. Resveratrol (3,4',5-trihydroxy-trans-stilbene) is a natural polyphenolic phytoalexin found in a variety of plants that influences various signal-transduction pathways which control apoptosis, cell growth and cell division, metastasis, angiogenesis and inflammation, and has an impact on cancer stages ranging from initiation to progression. In this work, molecular docking and molecular dynamics simulation method are employed to design resveratrol derivatives for COX-2 and 5-LOX enzymes. By attaching several functional groups on four different places of the resveratrol scaffold, the R group enumeration approach was employed to build four libraries of resveratrol derivatives. Thus, R group enumeration is done to focus on the enhancement of potency of compounds and other chemical characteristics like solubility. Drug-like filters such as REOS 1, 2, 3 and PAINS were applied to the libraries, generating a total of 5557 compounds. Drug-like filters such as REOS and PAINS-1, 2 and 3 were applied to the libraries, generating a total of 5557 compounds. All of these compounds were docked with both enzymes using the Glide SP and XP docking methods. Enrichment calculations were performed using 40 compounds from XP docking along with resveratrol, and 1000 decoy compounds from the DUD-E database to validate the docking protocol. The stability of the complexes was further studied using molecular dynamics simulation, radius of gyration, MM/GBSA, H bond monitoring and electrostatic potential surface (EPS). ADMET properties of compounds were studied using SwissADME and pkCSM server.Communicated by Ramaswamy H. Sarma.
在多种人类癌症中,环氧化酶-2(COX-2)和5-脂氧合酶(5-LOX)均上调并共同表达,促进癌细胞增殖和血管生成。白藜芦醇(3,4',5-三羟基反式芪)是一种天然多酚类植物抗毒素,存在于多种植物中,它影响控制细胞凋亡、细胞生长和细胞分裂、转移、血管生成和炎症的各种信号转导途径,并对从起始到进展的癌症阶段产生影响。在这项工作中,采用分子对接和分子动力学模拟方法设计针对COX-2和5-LOX酶的白藜芦醇衍生物。通过在白藜芦醇骨架的四个不同位置连接几个官能团,采用R基团枚举方法构建了四个白藜芦醇衍生物库。因此,进行R基团枚举以专注于提高化合物的效力以及其他化学特性,如溶解度。将诸如REOS 1、2、3和PAINS等类药过滤器应用于这些库,共生成5557种化合物。将诸如REOS和PAINS-1、2和3等类药过滤器应用于这些库,共生成5557种化合物。所有这些化合物都使用Glide SP和XP对接方法与两种酶进行对接。使用来自XP对接的40种化合物以及白藜芦醇,和来自DUD-E数据库的1000种诱饵化合物进行富集计算,以验证对接方案。使用分子动力学模拟、回转半径、MM/GBSA、氢键监测和静电势表面(EPS)进一步研究复合物的稳定性。使用SwissADME和pkCSM服务器研究化合物的ADMET性质。由Ramaswamy H. Sarma传达。