G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia.
Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., 142290 Pushchino, Russia.
Int J Mol Sci. 2024 Mar 26;25(7):3697. doi: 10.3390/ijms25073697.
Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus-host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.
病毒是任何生态系统中数量最多的生物形式。病毒性疾病不仅影响人类，还影响动植物。最近的大流行表明，科学界迅速应对挑战非常重要，包括对病毒威胁进行批判性评估，并制定适当的措施来应对这一威胁。世界各地的科学家正在做出巨大努力来解决这些问题。在计算机上进行模拟的方法，允许在许多情况下快速获得该领域的准确信息，是描述病毒活动各个方面的有效工具，包括病毒-宿主细胞相互作用，从而可以从分子水平深入了解病毒的作用机制。三维参考相互作用位点模型（3D-RISM）似乎是计算水合病毒最有效和最廉价的方法之一，因为该方法允许我们对水合病毒进行高效计算，同时保留液体环境和病毒结构的所有分子细节。大流行的挑战导致致力于水合病毒的 3D-RISM 计算数量迅速增加。为了为读者提供对该文献的总结，我们对 3D-RISM 计算进行了系统的综述，涵盖了自 2010 年以来的时期。我们讨论了 3D-RISM 结果的各种生物物理方面，并使用流感、肝炎和 SARS-CoV-2 等病毒的示例展示了该方法的能力、限制、成就和前景。
