A hydrophobic-interaction-based mechanism trigger docking between the SARS?COV?2 spike and angiotensin-converting enzyme 2

• 1、National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China
• 2、School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150001 China
• 3、Key LaboratA hydrophobic-interaction-based mechanism trigger docking between the COVID-19 spike and angiotensin-converting enzyme 2ory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, P. R. China
• 4、School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006, Australia
• 5、Shenzhen Etron Advanced Materials Research Institute Co., Ltd. Shenzhen 518035 China

Abstract：Published experimental evidence shows that affinity between SARS?COV?2 spike protein (S) and angiotensin converting enzyme 2 (ACE2) is about 10 to 20 times higher than the corresponding affinity of SARS virus spike protein. However, the molecular structures of the main-chain of the SARS?COV?2 spike and SARS spike are almost the same. Understanding physical mechanism that underlies the super affinity between the SARS?COV?2 spike protein and the ACE2 protein is the "urgent challenge" of developing blockers, vaccines and therapeutic antibodies against SARS?COV?2. Considering the mechanisms of hydrophobic interaction, hydration shell, surface tension, and the shielding effect of water molecules, this study reveals a hydrophobic-interaction-based by means of which spike proteins and ACE2 dock and bind together in an aqueous environment. There are a large number of hydrophobic sites on the surface of the spike protein and ACE2. Under the action of entropy and surface tension, the spike protein and ACE2 protein dock and bind together through the hydrophobic collapse between their surface, and the enthalpy-entropy compensation enable the hydrophilic residues get rid of their hydrogen-bonded water molecules and participate in the hydrophobic interaction of the binding process. We propose a design method to create a live attenuated virus by mutating several key amino acid residues to destroy the hydrophobic sites of the surface of the spike protein. Mutation of a small amount of residues can greatly reduce the hydrophobic binding of the coronavirus to the receptor, which may be significant reduce toxicity of the virus.

Keywords： SARS?COV?2 virus, spike protein (S), ACE2 protein, hydrated layer, hydrophobic interaction, enthalpy-entropy compensation