Bai Qifeng, Tan Shuoyan, Pérez-Sánchez Horacio, Feng Haixia, Feng Liya, Liu HuanXiang, Yao Xiaojun
Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
School of Pharmacy, Lanzhou University, Lanzhou, China.
Front Chem. 2019 Dec 17;7:851. doi: 10.3389/fchem.2019.00851. eCollection 2019.
The inactive conformations of glucagon receptor (GCGR) are widely reported by crystal structures that support the precision structure for drug discovery of type 2 diabetes. The previous study shows that the intracellular part is open in the glucagon-bound GCGR (glu-GCGR) and closed in the apo-GCGR by accelerated molecular dynamics (aMD) simulations. However, the crystal structure of GCGR in complex with partial agonist shows that the intracellular part is closed in the inactive conformation. To understand the differences between the studies of aMD simulations and crystal structure, the 2,500 ns conventional molecular dynamics (cMD) simulations are performed on the simulated model of glu-GCGR. The result shows that the transmembrane helices (TMH) 6 of glu-GCGR is outward ~4 Å to drive the intracellular part of glu-GCGR open until ~390 ns cMD simulations. The (TMH) 6 of glu-GCGR becomes closed after ~490 ns cMD simulations, which are consistent with the crystal structure of GCGR in complex with the partial agonist. To further elucidate the activation mechanism of GCGR deeply, the simulated models of glu-GCGR, apo-GCGR, and antagonist-bound GCGR (ant-GCGR) are constructed to perform 10 of parallel 300 ns aMD simulations, respectively. The results show that both of glu-GCGR and apo-GCGR can generate the open conformations of the intracellular part. But the glu-GCGR has the higher percentage of open conformations than apo-GCGR. The ant-GCGR is restricted to generate the open conformations of the intracellular part by antagonist MK-0893. It indicates that the glu-GCGR, apo-GCGR, and ant-GCGR can be distinguished by the aMD simulated method. Free energy landscape shows that the open conformations of the intracellular part of GCGR are in intermediate state. Our results show that aMD simulations enhance the space samplings of open conformations of GCGR via adding extra boost potential. It indicates that the aMD simulations are an effective way for drug discovery of GCGR.
胰高血糖素受体（GCGR）的无活性构象已被晶体结构广泛报道，这些晶体结构为2型糖尿病药物发现提供了精确结构。先前的研究表明，通过加速分子动力学（aMD）模拟，在结合胰高血糖素的GCGR（glu-GCGR）中细胞内部分是开放的，而在无配体的GCGR（apo-GCGR）中是关闭的。然而，与部分激动剂复合的GCGR的晶体结构表明，在无活性构象中细胞内部分是关闭的。为了理解aMD模拟研究与晶体结构之间的差异，对glu-GCGR的模拟模型进行了2500纳秒的传统分子动力学（cMD）模拟。结果表明，glu-GCGR的跨膜螺旋（TMH）6向外移动约4 Å，促使glu-GCGR的细胞内部分开放，直到约390纳秒的cMD模拟。在约490纳秒的cMD模拟后，glu-GCGR的（TMH）6变为关闭状态，这与与部分激动剂复合的GCGR的晶体结构一致。为了更深入地阐明GCGR的激活机制，构建了glu-GCGR、apo-GCGR和与拮抗剂结合的GCGR（ant-GCGR）的模拟模型，分别进行10次并行的300纳秒aMD模拟。结果表明，glu-GCGR和apo-GCGR都可以产生细胞内部分的开放构象。但glu-GCGR的开放构象百分比高于apo-GCGR。ant-GCGR受到拮抗剂MK-0893的限制，无法产生细胞内部分的开放构象。这表明通过aMD模拟方法可以区分glu-GCGR、apo-GCGR和ant-GCGR。自由能景观显示，GCGR细胞内部分的开放构象处于中间状态。我们的结果表明，aMD模拟通过添加额外的增强势来增强GCGR开放构象的空间采样。这表明aMD模拟是GCGR药物发现的有效方法。
