University of Lille, Inserm, U995 - LIRIC - Lille Inflammation Research International Center, ICPAL, 3 rue du Professeur Laguesse, BP-83, F-59006, Lille, France.
OncoWitan, Lille (Wasquehal), 59290, France.
Comput Biol Chem. 2020 Oct;88:107312. doi: 10.1016/j.compbiolchem.2020.107312. Epub 2020 Jun 20.
High Mobility Group Box 1 protein (HMGB1) is an abundant protein with multiple functions in cells, acting as a DNA chaperone and damage-associated molecular pattern molecule. It represents an attractive target for the treatment of inflammatory diseases and cancers. The plant natural product glycyrrhizin (GLR) is a well-characterized ligand of HMGB1 and a drug used to treat diverse liver and skin diseases. The drug is known to bind to each of the two adjacent HMG boxes of the non-glycosylated protein. In cells, HMGB1 is N-glycosylated at three asparagine residues located in boxes A and B, and these N-glycans are essential for the nucleocytoplasmic transport of the protein. But the impact of the N-glycans on drug binding is unknown. Here we have investigated the effect of the N-glycosylation of HMGB1 on its interaction with GLR using molecular modelling, after incorporation of three N-glycans on a Human HMGB1 structure (PDB code 2YRQ). Sialylated bi-antennary N-glycans were introduced on the protein and exposed in a folded or an extended conformation for the drug binding study. The docking of the drug was performed using both 18α- and 18β-epimers of GLR and the conformations and potential energy of interaction (ΔE) of the different drug-protein complexes were compared. The N-glycans do not shield the drug binding sites on boxes A and B but can modulate the drug-protein interaction, via both direct and indirect effects. The calculations indicate that binding of 18α/β-GLR to the HMG box is generally reduced when the protein is N-glycosylated vs. the non-glycosylated protein. In particular, the N-glycans in an extended configuration significantly weaken the binding of GLR to box-B. The effects of the N-glycans are mostly indirect, but in one case a direct contact with the drug, via a carbohydrate-carbohydrate interaction, was observed with 18β-GLR bound to Box-B of glycosylated HMGB1. For the first time, it is shown (at least in silico) that N-glycosylation, one of the many post-translational modifications of HMGB1, can affect drug binding.
高迁移率族蛋白 B1（HMGB1）是一种在细胞中具有多种功能的丰富蛋白质，作为 DNA 伴侣和损伤相关分子模式分子。它是治疗炎症性疾病和癌症的有吸引力的靶标。植物天然产物甘草酸（GLR）是 HMGB1 的一种特征配体，也是一种用于治疗多种肝脏和皮肤疾病的药物。已知该药物与未糖基化蛋白的两个相邻 HMG 盒中的每一个结合。在细胞中，HMGB1 在位于盒 A 和 B 中的三个天冬酰胺残基处被 N-糖基化，这些 N-聚糖对于蛋白质的核质转运是必不可少的。但是，糖基化对药物结合的影响尚不清楚。在这里，我们使用分子建模研究了 HMGB1 的 N-糖基化对其与 GLR 相互作用的影响，方法是在人类 HMGB1 结构（PDB 代码 2YRQ）上掺入三个 N-聚糖。在药物结合研究中，引入了唾液酸化的双触角 N-聚糖，并将其暴露在折叠或伸展构象中。使用 GLR 的 18α-和 18β-差向异构体进行药物对接，并比较了不同药物-蛋白质复合物的构象和相互作用的势能（ΔE）。聚糖不会屏蔽 A 和 B 盒上的药物结合位点，但可以通过直接和间接作用来调节药物-蛋白质相互作用。计算表明，与未糖基化的蛋白质相比，当蛋白质糖基化时，18α/β-GLR 与 HMG 盒的结合通常会降低。特别是，在伸展构象中的聚糖显着削弱了 GLR 与盒-B 的结合。聚糖的影响主要是间接的，但在一种情况下，通过与药物的直接接触，观察到与糖基化 HMGB1 的盒-B 结合的 18β-GLR 通过碳水化合物-碳水化合物相互作用与药物接触。首次表明（至少在计算机模拟中），HMGB1 的许多翻译后修饰之一的 N-糖基化可以影响药物结合。
