key: cord-0946563-iido1m2n authors: Lupala, Cecylia S.; Ye, Yongjin; Chen, Hong; Su, Xiao-Dong; Liu, Haiguang title: Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor date: 2021-12-17 journal: bioRxiv DOI: 10.1101/2021.12.10.472102 sha: 26c3285e0b901a2b666e2802db7b346ba28d28a9 doc_id: 946563 cord_uid: iido1m2n The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic. The recently occurred Omicron variant raised serious concerns about reducing the efficacy of vaccines and neutralization antibodies due to its vast mutations. We have modelled the complex structure of the human ACE2 protein and the receptor binding domain (RBD) of Omicron Spike protein (S-protein), and conducted atomistic molecular dynamics simulations to study the binding interactions. The analysis shows that the Omicron RBD binds more strongly to the human ACE2 protein than the original strain. The mutations at the ACE2-RBD interface enhance the tight binding by increasing hydrogen bonding interaction and enlarging buried solvent accessible surface area. hydrogen bonds formed between ACE2 and RBD O , about 10% more than 5.9 ± 2.4 116 hydrogen bonds observed in the wild type system. A closer examination on the specific 117 hydrogen bonds reveals that the Q493K and N501Y play important roles in forming new 118 hydrogen bonds (Table 1) . It is worthwhile to note that the hydrogen bonds are very 119 dynamical, and the total number of hydrogen bonds at any instant time fluctuates 120 significantly. Therefore, in the table we only listed seven hydrogen bonds that are 121 frequently observed during simulations, with the occupancy close to 20% or above. As 122 shown in Table 1 , the only hydrogen bond with occupancy below 20% is between ACE2 123 S19 and RBD A475 (occupancy = 18.73%). In the case of ACE2-RBD O , the next 124 frequently observed hydrogen bond is between K31 of ACE2 and W456 of RBD O with an 125 occupancy of 16.25% (not listed in Table 1 ). As shown in Table 1 , there are five common 126 stable hydrogen bonds observed in both the wild type and Omicron variant systems. The 127 mutations resulted in the loss of two hydrogen bonds: (1) the K417N mutation caused the 128 loss of hydrogen bonding with ACE2 residue D30, and (2) the Y505H mutation 129 significantly reduced its bonding to E37 of ACE2. The Q493K mutation not only maintains 130 the hydrogen bond between Q493 and E35 of ACE2 in the wild type complex, but also 131 adds the possibility of forming a new stable hydrogen bond between K493 and the D38 of 132 ACE2. The hydrogen bond between Y501 of RBD O and the Y41 of the ACE2 is also a new 133 hydrogen bond frequently observed in simulations. The hydrogen bond between the S19 of 134 ACE2 and the A475 of RBD O is stronger than that in the wild type system, although 135 neither residues were mutated in the Omicron variant. It is possibly influenced by the local 136 changes due to the S477N and T478K mutations. By comparing the occupancies, we 137 conclude that the hydrogen bonds between ACE2 and RBD O are more stable through the 138 simulations, and therefore resulting more hydrogen bonds on average. shown on the right column to compare the statistics between the wild type system and the 144 We computed the number of van der Waals contacts between the ACE2 and RBD, as well 155 as the buried surface area, to further assess the interactions between ACE2 and RBD. For 156 the wild type system, the two simulations yield 137 ± 12 contacts on average, while the The wild type ACE2-RBD and its Omicron variant were prepared using the CHARMM36 281 force fields, following the procedure of the CHARMM-GUI webserver. Each system was 282 solvated in 150 mM sodium chloride solvent with TIP3P water models. Steepest descent 283 algorithm was applied to minimize the system energy, then each system was equilibrated to 284 310.15 K (37 °C) within 125 ps. The temperature was maintained by Nose-Hoover scheme 285 with 1.0 ps coupling constant in the NVT ensemble (constant volume and temperature). 286 During the equilibration stage, harmonic restraint forces were applied to the molecules (400 287 kJ mol −1 nm −2 on backbone and 40 kJ mol −1 nm −2 on the side chain atoms) [24, 25] . 288 Subsequently, the harmonic restraints were removed and the NPT ensembles (constant 289 pressure and temperature) were simulated at one atmosphere pressure (10 5 Pa) and 310.15 K. The van der Waals interaction cutoff was set to 12.0 Å. Hydrogen atoms were constrained 296 using the LINCS algorithm [29] . 297 298 Analyses were carried out with tools in GROMACS (rmsd, rmsf, mindist, sasa) to examine 299 the system stability. The buried surface area is computed as 300 ΔA = AACE2 + ARBD -AACE2-RBD (1) 301 Where AACE2, ARBD, and AACE2-RBD are the solvent accessible surface area computed using 302 gmx sasa function. The mindist command was used to compute the residue distances, the 303 residue pairs with distance below 4.0 Å were considered as contacting residues. 304 VMD was used to analyze hydrogen bonding interactions [30] , with the following criteria: D-305 A distance cutoff=3.9 Å and D-H-A angle cutoff=20 degrees, where D,A,H are Donor atom, 306 Acceptor atom, and the Hydrogen atom linked to the Donor atom. Pymol was used for 307 molecular binding interface, water distributions, visualization, and rending model images 308 [30]. The adaptive Poisson-Boltzmann equation solver (APBS) was used to compute the 309 electrostatic potentials [31] . The authors declare no competing interests. 327 328 the binding dynamics between human ACE2 and the receptor binding domain 379 of SARS-CoV-2 spike protein Evolution of the 382 novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein 383 for risk of human transmission 388 Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of 389 ACE2 in vertebrates Computational insights into differential 392 interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 393 spike receptor binding domain Key residues of the receptor binding motif in the spike 397 protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies Structural and Functional Basis CoV-2 Entry by Using Human ACE2 Structure of the SARS-CoV-2 spike receptor-binding domain bound to the 405 ACE2 receptor Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights 408 into cocktail design against concerning variants Structure-based analyses of neutralization antibodies interacting with 412 naturally occurring SARS-CoV-2 RBD variants 1.1.529 escapes the majority of SARS-CoV-2 neutralizing antibodies of 418 diverse epitopes CHARMM-GUI Input Generator for NAMD, 423 GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the 424 CHARMM36 Additive Force Field A unified formulation of the constant temperature molecular dynamics 427 methods Canonical dynamics: Equilibrium phase-space distributions Polymorphic transitions in single crystals: A new molecular 431 dynamics method Gromacs: High performance molecular simulations through multi-level parallelism 435 from laptops to supercomputers, SoftwareX Particle mesh Ewald: An N·log(N) method for 438 Ewald sums in large systems LINCS: A Linear Constraint 441 Solver for molecular simulations VMD: Visual molecular dynamics Improvements to the APBS biomolecular solvation 450 software suite A hierarchical approach to all-atom protein loop prediction On the Role of the Crystal 456 Environment in Determining Protein Side-chain Conformations sars-cov-2-variant-of-concern (accessed December 9, 2021). [9] Science Brief: Omicron (B.