Institute of High Performance Computing, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore.
J Mol Graph Model. 2010 Sep;29(2):171-7. doi: 10.1016/j.jmgm.2010.05.009. Epub 2010 May 27.
Nanoparticles such as fullerenes and carbon nanotubes have been extensively studied for biomedical applications. In this paper, we report the design of carbon nanotubes as HIV-1 protease inhibitors. Docking and molecular dynamics calculations are performed using an atomistic model to explore the optimal interaction structure and free energy between the nanotube and HIV-1 protease. A coarse-grained model is then developed based on the atomistic model, allowing us to investigate the dynamic behaviors of the protease in the bound and unbound states. The dynamic process reveals that the carbon nanotube is able to bind to the active site of the protease and prevent the active flaps from opening up, thus blocking the function of the protease. This process is strongly influenced by the size of the nanotube. The binding of carbon nanotubes to an alternative binding site other than the active site is also explored. Therefore, carbon nanotube-based inhibitors have great potential for application as HIV-1 protease inhibitors.
纳米粒子，如富勒烯和碳纳米管，已被广泛研究用于生物医学应用。在本文中，我们报告了碳纳米管作为 HIV-1 蛋白酶抑制剂的设计。使用原子模型进行对接和分子动力学计算，以探索纳米管和 HIV-1 蛋白酶之间的最佳相互作用结构和自由能。然后，基于原子模型开发了一个粗粒模型，使我们能够研究在结合和未结合状态下蛋白酶的动态行为。动态过程表明，碳纳米管能够与蛋白酶的活性位点结合，并阻止活性瓣打开，从而阻断蛋白酶的功能。这个过程强烈地受到纳米管大小的影响。还探索了碳纳米管与活性位点以外的替代结合位点的结合。因此，基于碳纳米管的抑制剂作为 HIV-1 蛋白酶抑制剂具有很大的应用潜力。
