Molecular dynamics simulation:
To study the dynamic behavior, stability, and conformational flexibility
RBD-ACE2- naltrexone complex, all-atoms MD simulations were performed as
reported previously17,34,35. CHARMM36 force fields
were used for topology building of protein in GROMACSv2019.4
package36. The ligand topology was derived from CHARMM
General Force Field
(https://cgenff.umaryland.edu/)37. The structure
was solvated in a cubic water box in TIP3P water model. The system
charge was electro-neutralized by adding 0.15M NaCl to the solvated
system. To eliminate bad contacts in the complex system energy
minimization was done with the steepest descent algorithm in 5,000
steps. The non-hydrogen atoms of the ligands were restrained, and system
equilibration was done in two steps including NVT and NPT ensembles in
10 ns at 300 K in atmospheric condition (1 atm). Finally, production MD
was performed 100 ns at 300 K with a 2-femtosecond (fs) time step using
Leapfrog integrator. The resultant trajectory was explored to understand
the structural dynamics of the complex system through various utility
toolkits of GROMACS. Stability parameters including backbone root mean
square deviation (RMSD), the radius of gyration (Rg), Cα-root mean
squared fluctuations (RMSF), and intermolecular hydrogen bond (H-bond)
distributions were computed for the complex system. 2D graphs were
plotted using XMGrace, while, interaction images were plotted using
BIVIA DSV and PyMOL.
Statistical analysis: All the data presented is as mean ± SEM
of three individual experiments unless specified. Comparisons between
means were performed using Student t -test for unpaired data
within two conditions.