Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary.
Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
J Chem Inf Model. 2021 Jun 28;61(6):2926-2936. doi: 10.1021/acs.jcim.1c00200. Epub 2021 May 24.
Elucidation and improvement of the blood coagulant properties of heparin are the focus of intense research. In this study, we performed conformational analysis using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations on the heparin pentasaccharide analogue idraparinux, its disulfonatomethyl analogue, which features a slightly improved blood coagulation property, and a trisulfonatomethyl analogue, in which the activity has been totally abolished. As the ring conformation of the G subunit has been suggested as a major determinant of the biological properties, we analyzed the sugar ring conformations and dynamics of the interglycosidic linkages. We found that the conformation of the G ring is dominated by the S skewed boat next to the C chair in all three derivatives. Both the thermodynamics and the kinetics of the conformational states were found to be highly similar in the three derivatives. Molecular kinetic analysis showed that the S skewed boat state of the G ring is equally favorable in the three analogues, resulting in similar S populations. Also, the transition kinetics from the C chair to the S skewed boat was found to be comparable in the derivatives, which indicates a similar energy barrier between the two states of the G subunit. We also identified a slower conformational transition between the dominant C chair and the boat conformations on the E subunit. Both G and E ring flips are also accompanied by changes along the interglycosidic linkages, which take place highly synchronously with the ring flips. These findings indicate that conformational plasticity of the G ring and the dominance of the S skewed boat populations do not necessarily warrant the biological activity of the derivatives and hence the impact of other factors also needs to be considered.
阐明和改善肝素的凝血性质是目前研究的重点。在这项研究中，我们使用核磁共振（NMR）光谱和分子动力学（MD）模拟对肝素五糖类似物依达肝素、其具有略微改善的血液凝固性质的二磺甲醚类似物以及活性完全丧失的三磺甲醚类似物进行构象分析。由于 G 亚基的环构象被认为是生物性质的主要决定因素，我们分析了糖苷键间的糖环构象和动力学。我们发现，在所有三种衍生物中，G 环的构象均由紧邻 C 椅的 S 扭曲船型主导。三种衍生物的构象态的热力学和动力学都非常相似。分子动力学分析表明，G 环的 S 扭曲船型在三种类似物中同样有利，导致 S 种群相似。此外，我们还发现衍生物中从 C 椅到 S 扭曲船型的转变动力学具有可比性，这表明 G 亚基两种状态之间的能垒相似。我们还发现 E 亚基上的 C 椅和船型之间的构象转变较慢。G 和 E 环的翻转也伴随着糖苷键的变化，这与环的翻转高度同步发生。这些发现表明，G 环的构象可塑性和 S 扭曲船型种群的主导地位不一定保证衍生物的生物活性，因此还需要考虑其他因素的影响。
