Department of Biology, Faculty of Science, Shahid Chamran University, Ahvaz, Iran.
J Biomed Sci. 2013 Sep 12;20(1):67. doi: 10.1186/1423-0127-20-67.
Among viral enzymes, the human HIV-1 protease comprises the most interesting target for drug discovery. There are increasing efforts focused on designing more effective inhibitors for HIV-1 protease in order to prevent viral replication in AIDS patients. The frequent and continuous mutation of HIV-1 protease gene creates a formidable obstacle for enzyme inhibition which could not be overcome by the traditional single drug therapy. Nowadays, in vitro and in silico studies of protease inhibition constitute an advanced field in biological researches. In this article, we tried to simulate protease-substrate complexes in different states; a native state and states with whiskers deleted from one and two subunits. Molecular dynamic simulations were carried out in a cubic box filled with explicit water at 37°C and in 1atomsphere of pressure.
Our results showed that whisker truncation of protease subunits causes the dimer structure to decrease in compactness, disrupts substrate-binding site interactions and changes in flap status simultaneously.
Based on our findings we claim that whisker truncation even when applied to a single subunit, threats dimer association which probably leads to enzyme inactivation. We may postulate that inserting a gene to express truncated protease inside infected cells can interfere with protease dimerization. The resulted proteases would presumably have a combination of native and truncated subunits in their structures which exert no enzyme activities as evidenced by the present work. Our finding may create a new field of research in HIV gene therapy for protease inhibition, circumventing problems of drug resistance.
在病毒酶中，人类 HIV-1 蛋白酶是药物发现最有趣的目标。为了防止艾滋病患者体内病毒复制，人们越来越关注设计更有效的 HIV-1 蛋白酶抑制剂。HIV-1 蛋白酶基因的频繁和持续突变给酶抑制带来了巨大的障碍，这是传统的单一药物治疗无法克服的。如今，蛋白酶抑制的体外和计算研究构成了生物研究的一个先进领域。在本文中，我们试图模拟不同状态下的蛋白酶-底物复合物；一个天然状态和从一个和两个亚基中删除须状结构的状态。分子动力学模拟在一个充满显式水的立方盒中进行，温度为 37°C，压力为 1 个大气压。
我们的结果表明，蛋白酶亚基的须状结构截断导致二聚体结构的紧凑性降低，破坏了底物结合位点的相互作用，并同时改变了瓣状态。
根据我们的发现，我们声称须状结构截断即使应用于单个亚基，也会威胁到二聚体的缔合，这可能导致酶失活。我们可以假设，在感染细胞中插入表达截断蛋白酶的基因可以干扰蛋白酶的二聚化。由此产生的蛋白酶可能在其结构中具有天然和截断亚基的组合，正如本工作所证明的那样，它们没有酶活性。我们的发现可能为 HIV 基因治疗中的蛋白酶抑制开辟一个新的研究领域，规避耐药性问题。
