Oral presentation
29
In silico STUDY OF BUFADIENOLIDES
FROM Bufo viridis VENOM
M.B. Kayumov, Z.Zh. Mirakhmetova, N.R. Mukhamedov, Sh.Ya. Mirzaakhmedov
Institute of Bioorganic Chemistry, 100125, Tashkent, Mirzo Ulugbek street 83
e mail: mirzaakhmedov@mail.ru
In recent years, there has been increasing attention to study active substances isolated
from the natural origin which are effectively inhibited Sars-Cov-2. The main protease
(M-pro) of Sars-Cov-2 is one of the perfect targets to combat against the virus. Last
three years there has been demonstrated several synthetic
drugs which can inhibit M-
pro. Bufadienolides from toad venoms has anti-cancer, anti-bacterial, anti-arrhythmic
and anti-viral activities. Therefore, in-depth physicochemical and pharmaco-biological
evaluation of bufadienolides is of great interest. Besides, bufadienolides including
bufalin, arenobufagin, marinobufagin, telocinobufagin, bufarenogin, gamabufotalin
extracted from Central Asian green toad,
Bufo viridis
venom still in demand of deeper
investigation as an anti-Sars-Cov-2 compound.
In this work, we presented
in silico
analysis of 6 bufadienolides from toad
Bufo viridis
venom applying molecular docking
and molecular dynamics studies to study the possible receptor-ligand complex binding
types and structural integrity of the complex. For free energy calculation, we used an
umbrella sampling simulation.
For docking analysis used MOE 2014.0901 software and 3D structures of
bufadienolides obtained from PubChem database in SDF and MOL format. The x-ray
structure of 3CL protease (PDB ID: 7KPH) was downloaded from RCSB Protein Data
Bank and protein was prepared using the software default Structure Preparation
application. MD simulation carries out by GROMACS-2020 software package applying
the CHARMM27 all-atom force field.
To check the stability, of the protein-ligand
complex, we calculated the root mean square deviation (RMSD), and root mean square
fluctuations (RMSF). The final frame of the complex was extracted for
umbrella
sampling (US) simulation. The complex was enclosed in an appropriately sized box,
and the centre of mass of the ligand was then pulled along the y-axis by applying an
external force, while the protein was restrained and served as a reference for tension
modelling. In the pulling simulation, a spring constant of 1000 kJ/(mol*nm
2
) and
pulling at a rate of 0.01 nm/ps for 500 ps were used. We identified 50 umbrella
windows each 0.1nm then windows stabilized for 100 ps and then a 10 ns US
simulation was performed. Among ligands the gamabufatalin in complex with 3CL-
protease presented short equilibration time (5ns) at the 0.25-0.75 A
o
with low range of
RMSD value around 0.5 A
o
. Reduced RMSF tones were obtained at residues 40-56,
130-150 and 180-190 of the active sites due to the interaction of the ligand with pocket
amino acids. The free energy profile in the US simulation was calculated as -49.8
kJ/mol for the ligand-protein, indicating the formation of the most stable complex.MD
and US simulation data analysis results exhibited that, the gamabufatalin might be an
effective inhibitor against to SARS-Cov-2 main protease. Nowadays detailed
in-vitro
analysis of bufadienolides are going on.