Department of Chemistry, Payame Noor University, Tehran, 19395-4697, IR, Iran.
J Mol Model. 2023 Jun 16;29(7):213. doi: 10.1007/s00894-023-05594-5.
Using the molecular dynamics simulation method, the adsorption of folic acid as a drug with diphenylalanine peptide nanohole as an efficient nanodrug delivery system was investigated computationally. It focuses on the structural properties, drug loading capacity in the carrier, intermolecular interactions, and drug encapsulation behaviors. The results show that the average number of hydrogen bonds between diphenylalanine and folic acid will increase when the system reaches equilibrium. In addition, by increasing the weight concentration of folic acid from 0.3 to 0.9%, the number of hydrogen bond between them increases about 18%. In other words, hydrogen bonding can play an effective role in the binding of folic acid to the drug carrier. The results of the radial distribution function of water molecules around the carrier mass center show that its effective radius is around 1.2 nm (or 12 Å), which is in a good agreement with the results obtained from the hydrodynamic radius.
The initial structures were optimized in Amber molecular mechanics using Gaussian 09 software in aqueous medium in DFT/B3LYP/6-31 g(d). The molecular structure of folic acid was obtained from the PubChem database. The initial parameters are embedded in AmberTools. To calculate partial charges, restrained electrostatic potential (RESP) method was used. Gromacs 2021 software, modified water model (SPC/E), and Amber 03 force field have been used in all simulations. VMD software was used to view simulation photos.
使用分子动力学模拟方法，从计算角度研究了叶酸作为药物与二苯丙氨酸肽纳米孔作为高效纳米药物传递系统的吸附作用。重点研究了载体中的结构特性、药物负载能力、分子间相互作用和药物包封行为。结果表明，系统达到平衡时，二苯丙氨酸与叶酸之间的平均氢键数量将会增加。此外，通过将叶酸的重量浓度从 0.3%增加到 0.9%，它们之间氢键的数量增加了约 18%。换句话说，氢键可以在叶酸与药物载体的结合中发挥有效作用。载体质心周围水分子的径向分布函数的结果表明，其有效半径约为 1.2nm（或 12Å），与水动力半径的结果吻合较好。
在 Amber 分子力学中使用 Gaussian 09 软件在含水介质中进行初始结构的优化，在 DFT/B3LYP/6-31g(d)水平上进行。叶酸的分子结构从 PubChem 数据库中获得。初始参数被嵌入到 AmberTools 中。为了计算部分电荷，使用了受限静电势（RESP）方法。在所有模拟中都使用了 Gromacs 2021 软件、改进的水模型（SPC/E）和 Amber 03 力场。使用 VMD 软件查看模拟照片。
