Homology Modelling, Docking-based Virtual Screening, ADME Properties, and Molecular Dynamics Simulation for Identification of Probable Type II Inhibitors of AXL Kinase
Authors: Bhojwani Heena R. , Joshi Urmila J. 
Published: October 2021

Background:

AXL kinase is an important member of the TAM family for kinases which is
involved in most cancers. Considering its role in different cancers due to its pro-tumorigenic effects and its
involvement in the resistance, it has gained importance recently. Majority of research carried out is on Type I
inhibitors and limited studies have been carried out for Type II inhibitors. Taking this into consideration, we
have attempted to build Homology models to identify the Type II inhibitors for the AXL kinase.

Methods:

Homology Models for DFG-out C-helix-in/out state were developed using SWISS Model,
PRIMO, and Prime. These models were validated by different methods and further evaluated for stability
by molecular dynamics simulation using Desmond software. Selected models PED1-EB and PEDI1-EB
were used for the docking-based virtual screening of four compound libraries using Glide software. The
hits identified were subjected to interaction analysis and shortlisted compounds were subjected to Prime
MM-GBSA studies for energy calculation. These compounds were also docked in the DFG-in state to
check for binding and elimination of any compounds that may not be Type II inhibitors. The Prime energies
were calculated for these complexes as well and some compounds were eliminated. ADMET studies
were carried out using Qikprop. Some selected compounds were subjected to molecular dynamics simulation
using Desmond for evaluating the stability of the complexes.

Results:

Out of 78 models inclusive of both DFG-out C-helix-in and DFG-out C-helix-out, 5 models were
identified after different types of evaluation as well as validation studies. 1 model representing each type
(PED1-EB and PEDI1-EB) was selected for the screening studies. The screening studies resulted in the
identification of 29 compounds from the screen on PED1-EB and 10 compounds from the screen on
PEDI1-EB. Hydrogen bonding interactions with Pro621, Met623, and Asp690 were observed for these
compounds primarily. In some compounds, hydrogen bonding with Leu542, Glu544, Lys567, and
Asn677 as well as pi-pi stacking interactions with either Phe622 or Phe691 were also seen. 4 compounds
identified from PED1-EB screen were subjected to molecular dynamics simulation and their interactions
were found to be consistent during the simulation. 2 compounds identified from PEDI1-EB screen were
also subjected to the simulation studies, however, their interactions with Asp690 were not observed for a
significant time and in both cases differed from the docked pose.

Conclusion:

Multiple models of DFG-out conformations of AXL kinase were built, validated and used
for virtual screening. Different compounds were identified in the virtual screening, which may possibly
act as Type II inhibitors for AXL kinase. Some more experimental studies can be done to validate these
findings in future. This study will play a guiding role in the further development of the newer Type II
inhibitors of the AXL kinase for the probable treatment of cancer.