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Quantum molecular modelling of ibuprofen bound to human serum albumin

机译:布洛芬与人血清白蛋白结合的量子分子模型

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The binding of the nonsteroidal anti-inflammatory drug ibuprofen (IBU) to human serum albumin (HSA) is investigated using density functional theory (DFT) calculations within a fragmentation strategy. Crystallographic data for the IBU-HSA supramolecular complex shows that the ligand is confined to a large cavity at the subdomain IIIA and at the interface between the subdomains IIA and IIB, whose binding sites are FA3/FA4 and FA6, respectively. The interaction energy between the IBU molecule and each amino acid residue of these HSA binding pockets was calculated using the Molecular Fractionation with Conjugate Caps (MFCC) approach employing a dispersion corrected exchange-correlation functional. Our investigation shows that the total interaction energy of IBU bound to HSA at binding sites of the fatty acids FA3/FA4 (FA6) converges only for a pocket radius of at least 8.5 angstrom, mainly due to the action of residues Arg410, Lys414 and Ser489 (Lys351, Ser480 and Leu481) and residues in nonhydrophobic domains, namely Ile388, Phe395, Phe403, Leu407, Leu430, Val433, and Leu453 (Phe206, Ala210, Ala213, and Leu327), which is unusual. Our simulations are valuable for a better understanding of the binding mechanism of IBU to albumin and can lead to the rational design and the development of novel IBU-derived drugs with improved potency.
机译:非甾体抗炎药布洛芬(IBU)与人血清白蛋白(HSA)的结合作用是通过片段化策略内的密度泛函理论(DFT)计算来研究的。 IBU-HSA超分子复合物的晶体学数据表明,该配体被限制在子结构域IIIA以及子结构域IIA和IIB之间的界面处的大空腔中,其结合位点分别为FA3 / FA4和FA6。 IBU分子与这些HSA结合口袋的每个氨基酸残基之间的相互作用能通过使用具有色散校正交换相关功能的缀合帽分子分级(MFCC)方法进行计算。我们的研究表明,在脂肪酸FA3 / FA4(FA6)的结合位点与HSA结合的IBU的总相互作用能仅在至少8.5埃的口袋半径处收敛,这主要是由于残基Arg410,Lys414和Ser489的作用(Lys351,Ser480和Leu481)以及非疏水域中的残基,即Ile388,Phe395,Phe403,Leu407,Leu430,Val433和Leu453(Phe206,Ala210,Ala213和Leu327),这是不常见的。我们的模拟对于更好地了解IBU与白蛋白的结合机制非常有价值,并且可以导致合理设计和开发具有更高效能的新型IBU衍生药物。

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