The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people across the globe and created not only a health emergency but also a financial crisis. This virus attacks on the angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membrane. The spike protein of the virus binds to this receptor which is a critical step of infection. A molecule which can specifically stop this binding could be a potential therapeutic. In this study, we have tested 12 potential peptides which can bind to the receptor binding domain (RBD) of the spike protein of the virus and thus can potentially inhibit the binding of the latter on ACE2 receptor. These peptides are screened based on their binding with RBD of the spike protein and aqueous stability, obtained using several atomistic molecular dynamic simulations. The potential of mean force calculation of two most promising peptides confirmed their binding to the RBD of the spike protein. Furthermore, these two potential peptides were tested for their use in a biosensing application for SARS-CoV-2 detection. Two types of biosensing platforms, a graphene sheet and a carbon nano tube (CNT), were tested. The peptides were modified in order to functionalize the graphene and CNT. Based on the interaction between the substrate, peptide and spike protein, the utility of screened peptide for a given bio sensing platform is discussed and recommended.

中文翻译：

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与SARS-CoV-2受体结合域（RBD）结合的肽的计算机模拟设计及其在SARS-CoV-2检测的生物传感器开发中的实用性

严重的急性呼吸综合症冠状病毒2（SARS-CoV-2）感染了全球数以百万计的人，不仅造成了紧急医疗事件，而且造成了金融危机。该病毒攻击位于宿主细胞膜表面的血管紧张素转换酶2（ACE2）受体。病毒的刺突蛋白与该受体结合，这是感染的关键步骤。可以特异性终止这种结合的分子可能是潜在的治疗剂。在这项研究中，我们测试了12种可能的肽，它们可以与病毒的突突蛋白的受体结合域（RBD）结合，因此可以潜在地抑制后者与ACE2受体的结合。根据它们与刺突蛋白的RBD结合和水稳定性来筛选这些肽，使用几个原子分子动力学模拟获得。两种最有前途的肽的平均力计算潜力证实了它们与刺突蛋白的RBD结合。此外，测试了这两种潜在的肽在用于SARS-CoV-2检测的生物传感应用中的用途。测试了两种类型的生物传感平台，即石墨烯片和碳纳米管（CNT）。修饰肽以功能化石墨烯和CNT。基于底物，肽和刺突蛋白之间的相互作用，讨论并推荐了用于给定生物传感平台的筛选肽的实用性。测试了这两种潜在的肽在用于SARS-CoV-2检测的生物传感应用中的用途。测试了两种类型的生物传感平台，即石墨烯片和碳纳米管（CNT）。修饰肽以功能化石墨烯和CNT。基于底物，肽和刺突蛋白之间的相互作用，讨论并推荐了用于给定生物传感平台的筛选肽的实用性。测试了这两种潜在的肽在用于SARS-CoV-2检测的生物传感应用中的用途。测试了两种类型的生物传感平台，即石墨烯片和碳纳米管（CNT）。修饰肽以功能化石墨烯和CNT。基于底物，肽和刺突蛋白之间的相互作用，讨论并推荐了用于给定生物传感平台的筛选肽的实用性。