School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia.
Pharmaceutical Design and Simulation (PhDS) Laboratory, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia.
Molecules. 2021 Feb 18;26(4):1079. doi: 10.3390/molecules26041079.
Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA-FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
叶酸受体 alpha（FRα）因其在癌上皮组织中的过度表达而被称为许多癌症的生物标志物。叶酸（FA）与 FRα 活性位点的结合亲和力为设计更特异的 FRα 靶点提供了基础。杂环已被证明与许多受体相互作用，并且对体内的代谢和生物过程很重要。设计了 19 种带有各种杂环取代的 FA 类似物，以提高对 FRα 的亲和力。分子对接用于研究与 FA、甲氨蝶呤（MTX）和培美曲塞（PTX）相比，设计类似物的结合亲和力。在 19 种 FA 类似物中，带有四唑环（FOL03）和苯并噻吩环（FOL08）的类似物显示出最负的结合能，并且能够通过氢键与活性位点的氨基酸相互作用，与 ASP81 和 SER174 相互作用。因此，对 FOL03、FOL08 进行了 100ns 的分子动力学（MD）模拟，与 FA、MTX 和 PTX 进行了比较。FOL03 和 FOL08 的均方根偏差（RMSD）和均方根波动（RMSF）显示出与 FA 相似的明显收敛，它们都从蝶啶部分进入结合口袋（活性位点），而谷氨酸部分在 MD 模拟过程中卡在 FRα 口袋入口处。分子力学泊松-玻尔兹曼表面可及性（MM-PBSA）和氢键分析表明，与 FA 和 PTX 相比，FOL03 和 FOL08 产生了更负的自由结合能和静电能，并且都与 ASP81 形成了比 FA 更强的氢键相互作用，具有出色的氢键分布，使它们紧密结合在口袋中。此外，口袋体积计算表明，FOL03 和 FOL08 在 FRα 口袋中的活性位点体积小于 FA-FRα 系统，这表明在 MD 模拟过程中，这些新的 FA 类似物与蛋白质活性位点残基之间的相互作用比 FA 更强。
