Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

The spike protein of SARS-CoV-2 binds to ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two ab initio quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q⁴⁹³, Y⁵⁰⁵, Q⁴⁹⁸, N⁵⁰¹, T⁵⁰⁰, N⁴⁸⁷, Y⁴⁴⁹, F⁴⁸⁶, K⁴¹⁷, Y⁴⁸⁹, F⁴⁵⁶, Y⁴⁹⁵, and L⁴⁵⁵ have been identified as hotspots in RBD, while those in ACE2 are K³⁵³, K³¹, D³⁰, D³⁵⁵, H³⁴, D³⁸, Q²⁴, T²⁷, Y⁸³, Y⁴¹, E³⁵, and E³⁷. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q⁴⁹³, N⁵⁰¹, F⁴⁸⁶, K⁴¹⁷, and F⁴⁵⁶ in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N⁴⁸⁷, Q⁴⁹³, Y⁴⁴⁹, T⁵⁰⁰, G⁴⁹⁶, G⁴⁴⁶ and G⁵⁰² in RBD form pairs via specific hydrogen bonding with Q²⁴, H³⁴, E³⁵, D³⁸, Y⁴¹, Q⁴² and K³⁵³ in ACE2.