Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA.
Proteins. 2012 Apr;80(4):1110-22. doi: 10.1002/prot.24012. Epub 2012 Jan 31.
The current challenge in designing effective drugs against HIV-1 is to find novel candidates with high potency, but with a lower susceptibility to mutations associated with drug resistance. Trying to address this challenge, we developed in our previous study (Ishikita and Warshel, Angew Chem Int Ed Engl 2008; 47:697-700) a novel computational strategy for fighting drug resistance by predicting the likely moves of the virus through constraints on binding and catalysis. This has been based on calculating the ratio between the vitality values ((K(i) k(cat)/K(M))(mutant)/(K(i) k(cat)/K(M))(wild-type)) and using it as a guide for predicting the moves of the virus. The corresponding calculations of the binding affinity, K(i), were carried out using the semi-macroscopic version of the protein dipole Langevin dipole (PDLD/S) in its linear response approximation (LRA) in its β version (PDLD/S-LRA/β). We also calculate the proteolytic efficiency, k(cat)/K(M), by evaluating the transition state (TS) binding free energies using the PDLD/S-LRA/β method. Here we provide an extensive validation of our strategy by calculating the vitality of six existing clinical and experimental drug candidates. It is found that the computationally determined vitalities correlate reasonably well with those derived from the corresponding experimental data. This indicates that the calculated vitality may be used to identify mutations that would be most effective for the survival of the virus. Thus, it should be possible to use our approach in screening for mutations that would provide the most effective resistance to any proposed antiviral drug. This ability should be very useful in guiding the design of drug molecules that will lead to the slowest resistance.
当前设计有效抗 HIV-1 药物的挑战在于寻找具有高活性但突变易感性较低的新型候选药物,这些突变与药物耐药性相关。为了应对这一挑战,我们在之前的研究中开发了一种新的计算策略,通过对结合和催化的限制来预测病毒可能的变化,从而对抗药物耐药性。这是基于计算活力值的比值(((K(i) k(cat)/K(M))(mutant)/(K(i) k(cat)/K(M))(wild-type))),并将其用作预测病毒运动的指南。使用其线性响应近似 (LRA) 的β版本 (PDLD/S-LRA/β),我们还通过评估过渡态 (TS) 结合自由能来计算蛋白偶极 Langevin 偶极子 (PDLD/S) 的半宏观版本的结合亲和力,K(i)。在此,我们通过计算六种现有的临床和实验性药物候选物的活力来广泛验证我们的策略。结果发现,计算出的活力与相应的实验数据相当吻合。这表明计算出的活力可用于鉴定对病毒存活最有效的突变。因此,我们可以使用这种方法筛选出对任何拟议的抗病毒药物最有效的耐药性突变。这种能力对于指导设计导致耐药性最慢的药物分子非常有用。