Malathi Jambulingam, Umashankar Vetrivel, Sathyabaarathi Ravichandran, Muthukumaran Sivashanmugan, Ishwarya Murali, Madhavan Hajib Narahari
Bioinformation. 2011 Feb 7;5(9):390-5. doi: 10.6026/97320630005390.
This study reports the probable impact of the coupled mutations observed in our clinical isolate of HCMV UL54 polymerase, through structural bioinformatics approaches. The reported variant was found to be resistant to Ganciclovir (GCV) as per the clinical records. The presence of Glutamine deletion at 639 (Glu639) and a mis sense mutation of Serine 655 Leucine (Ser655Leu) in UL54 were identified by DNA sequencing and were predicted to lie in the DNA polymerase type-II domain. Docking simulation studies of the phosphorylated forms of Ganciclovir (GCV), Cidofovir (CDV) and Foscarnet (PFA) with the reported mutants showed significant variation in terms of binding affinity and inhibitory constant (Ki) in comparison to wild type UL54. The findings of this study revealed that the observed coupled mutation could potentially induce allosteric effects in the binding pockets of UL54 and thereby alter the drug binding affinity. In specific, it was observed that this coupled mutation could confer changes in the binding affinity of GCV and PFA by altering the binding energies and inhibitory constants to -0.88Kcal/mol and 226.71mM, -5.81Kcal/mol and 54.83µM, respectively, in comparison to Wild Type. On the other hand, CDV showed increased susceptibility for the reported mutant with a binding energy of -6.16Kcal/mol and inhibitory constant of 30.47µM.
本研究通过结构生物信息学方法，报告了在我们的人巨细胞病毒UL54聚合酶临床分离株中观察到的耦合突变可能产生的影响。根据临床记录，所报告的变体对更昔洛韦（GCV）具有抗性。通过DNA测序鉴定出UL54中639位谷氨酰胺缺失（Glu639）和丝氨酸655突变为亮氨酸（Ser655Leu），并预测这些突变位于DNA聚合酶II型结构域。对更昔洛韦（GCV）、西多福韦（CDV）和膦甲酸钠（PFA）的磷酸化形式与所报告的突变体进行对接模拟研究，结果显示与野生型UL54相比，在结合亲和力和抑制常数（Ki）方面存在显著差异。本研究结果表明，观察到的耦合突变可能在UL54的结合口袋中潜在地诱导变构效应，从而改变药物结合亲和力。具体而言，观察到这种耦合突变可通过将结合能和抑制常数分别改变为-0.88千卡/摩尔和226.71毫摩尔、-5.81千卡/摩尔和54.83微摩尔，从而使GCV和PFA的结合亲和力发生变化，与野生型相比。另一方面，CDV对所报告的突变体表现出更高的敏感性，结合能为-6.16千卡/摩尔，抑制常数为30.47微摩尔。
