Molecular Dynamics Simulations Indicate the SARS-CoV-2 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design

Maria Bzówka; Karolina Mitusinska; Agata Raczynska; Aleksandra Samol; Jack Tuszynski; Artur Góra

The H++ server [45] was used to protonate the SARS-CoV-2 and SARS-CoV main proteases' structures (PDB IDs: 6lu7, 6y2e, 2amq and 1q2w, respectively) using standard parameters and pH 7.4. The missing 4-amino-acids-long loop of the 1q2w model was added using the corresponding loop of the 6lu7 model. Water molecules were placed using the combination of 3D-RISM [46] and the Placevent algorithm [47] . The AMBER 18 LEaP [48] was used to immerse models in a truncated octahedral box of TIP3P water molecules and prepare the systems for simulation using the ff14SB force field41. Additionally, 4 and 3 Na + ions were added to the SARS-CoV-2 and the SARS-CoV, respectively. AMBER 18 software [48] was used to run 2 μs simulations of both systems. The minimisation procedure consisted of 2000 steps, involving 1000 steepest descent steps followed by 1000 steps of conjugate gradient energy minimisation, with decreasing constraints on the protein backbone (500, 125 and 25 kcal x mol-1 x Å2) and a final minimisation with no constraints of conjugate gradient energy minimization. Next, gradual heating was performed from 0 K to 300 K over 20 ps using a Langevin thermostat with a temperature coupling constant of 1.0 ps in a constant volume periodic box. Equilibration and production stages were run using the constant pressure periodic boundary conditions for 1 ns with 1 fs step and 50 ns with a 2 fs time step, respectively. Constant temperature was maintained using the weak-coupling algorithm for 50 ns of the production simulation time, with a temperature coupling constant of 1.0 ps. Long-range electrostatic interactions were modelled using the Particle Mesh Ewald method with a non-bonded cut-off of 10 Å and the SHAKE algorithm. The coordinates were saved at an interval of 1 ps.