Cubuk Hasan, Ozbil Mehmet, Cakir Hatir Pinar
Istanbul Arel University, Department of Biomedical Engineering, Bioinspired Functional Polymers and Nanomaterials Laboratory, 34537 Buyukcekmece, Istanbul, Turkey.
Gebze Technical University, Institute of Biotechnology, 41400 Gebze, Kocaeli, Turkey.
Comput Theor Chem. 2021 May;1199:113215. doi: 10.1016/j.comptc.2021.113215. Epub 2021 Mar 16.
Today, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused a severe outbreak worldwide. There are still several challenges in COVID-19 diagnoses, such as limited reagents, equipment, and long turnaround times. In this research, we propose to design molecularly imprinted polymers as a novel approach for the rapid and accurate detection of SARS-CoV-2. For this purpose, we investigated molecular interactions between the target spike protein, receptor-binding domain of the virus, and the common functional monomers used in molecular imprinting by a plethora of computational analyses; sequence analysis, molecular docking, and molecular dynamics (MD) simulations. Our results demonstrated that AMPS and IA monomers gave promising results on the SARS-CoV-2 specific TEIYQAGST sequence for further analysis. Therefore, we propose an epitope approach-based synthesis route for specific recognition of SARS-CoV-2 by using AMPS and IA as functional monomers and the peptide fragment of the TEIYQAGST sequence as a template molecule.
如今，严重急性呼吸综合征冠状病毒2（SARS-CoV-2）最近在全球范围内引发了严重疫情。新型冠状病毒肺炎（COVID-19）诊断仍存在诸多挑战，如试剂有限、设备不足以及周转时间长等问题。在本研究中，我们提议设计分子印迹聚合物，作为一种快速准确检测SARS-CoV-2的新方法。为此，我们通过大量计算分析，即序列分析、分子对接和分子动力学（MD）模拟，研究了目标刺突蛋白、病毒受体结合结构域与分子印迹中常用功能单体之间的分子相互作用。我们的结果表明，2-丙烯酰胺基-2-甲基丙磺酸（AMPS）和衣康酸（IA）单体在SARS-CoV-2特异性TEIYQAGST序列上给出了有前景的结果，可供进一步分析。因此，我们提出一种基于表位方法的合成路线，以使用AMPS和IA作为功能单体，TEIYQAGST序列的肽片段作为模板分子来特异性识别SARS-CoV-2。
