6 / 27
Page 61
allied
academies
J Pharmacol Ther Res 2017 Volume 1 Issue 2
November 02-03, 2017 Chicago, USA
4
th
International Congress on
International Conference and Exhibition on
Drug Discovery, Designing and Development
Biochemistry, Molecular Biology: R&D
&
Introduction:
The development of drug resistance is a
leading cause of treatment failures in many cancers. MAPK
is an important cell signaling pathway. Many cancer drugs
are designed to induce MAPK inhibition (MAPKi). Although
MAPKi reduces cancer growth and migration, it is usually
accompanied by the establishment of bypass signaling
mediated by certain Receptor Tyrosine Kinases (RTKs). As a
result, most patients acquire a resistance to MAPKi within
a year. The simultaneous inhibition of implicated RTKs and
MAPK is needed to overcome drug resistance. Most kinase
inhibitors bind to the kinase ATP-binding site. The high
homology of these sites among different kinases makes
them challenging to target specifically. The specificity is
important, since drugs that indiscriminately inhibit several
kinases may harm healthy cells. Unlike ATP-competitive
inhibitors, an allosteric inhibitor can retain its inhibitory
effectiveness at various ATP concentrations. Allosteric sites
vary between various kinases and thus allow a highly specific
binding with fewer side effects. Patients that develop
MAPKi resistance show a significant accumulation of certain
RTKs, such as AXL and MET. AXL and MET are involved in
many cellular processes. Several inhibitors of these kinases
have been found. However, they all bind to the kinases’
catalytic sites and, thus, lack selectivity. This work focuses
on computational design of small druglike molecules that
could potentially allosterically bind AXL and MET and, thus,
prevent the creation of signaling that would bypass MAPK
inhibition.
Materials and Methods:
The following software and servers
were used to analyze AXL and MET and their putative
inhibitors: Protein Data Bank (PDB), Deep View, ArgusLab,
Molinspiration, and Osiris Data Warrior. Three-dimensional
structures of AXL and MET were obtained from the PDB
(5TC0 and 5MJA, respectively). The DeepView program
was used to simultaneously analyze the active sites, atomic
distances, H-bonds, and charge densities of the molecules.
The Argus Lab programwas employed to analyze the docking
sites and perform docking calculations. Druglike properties
of designed small molecules were evaluated using the
Molinspiration and Osiris Data Warrior programs. ATP-
competitive inhibitors of AXL and MET were uploaded in
ArgusLab and docked to the kinases. Fig. 1 a) and b) show
the ATP pockets of AXL and MET, respectively, bound to
their known ATP-competitive inhibitors. The figures show
the AXL and MET residues within 6.0 Å from their respective
inhibitors.The known inhibitors of AXL and MET were used as
starting templates to computationally design new molecules
that could potentially bind both AXL and MET. Atomic
substitutions were done in the original inhibitors to achieve
improved druglikeness of the newly designed molecules.
Molecules that showed optimal druglike properties were
chosen for further docking studies. The designed molecules
were reconstructed and optimized in ArgusLab by using
the Semiempirical Geometry Optimization. The Argus Dock
function was used to dock the molecules in AXL and MET. The
AScore function and a 0.4 Å grid resolution were used for the
docking calculations. ArgusLab evaluated binding affinities of
the designed molecules to the AXL and MET kinases.
Results and Discussion:
One of the designed molecules was
found to have optimal druglike properties and no indicated
toxicities. The molecule formed stable complexes with AXL
andMET, binding each allosterically. Fig. 2 shows themolecule
docked to an allosteric site of AXL. The binding changed
the configuration of the catalytic site and so prevented the
binding of the ATP molecule in the site. The ATP molecule
bonded in a new location. Fig. 3 shows the molecule docked
allosterically in MET. The ATP molecule again bonded outside
the catalytic site.
Conclusions:
This work addresses computational design of
putative allosteric inhibitors of the AXL and MET kinases.
A designed molecule with promising druglike properties
bonded to allosteric sites of the kinases. The binding
caused conformational changes in the catalytic sites,
which prevented the ATP molecule from binding there.
The development of small molecule inhibitors that could
simultaneously allosterically bind AXL and MET shows a
promise for preventing the bypass signaling mediated by AXL
or MET.
e:
dalafave@tcnj.eduComputer aided design of small molecule inhibitors of Receptor Tyrosine Kinases (RTKs)
D S Dalafave
The College of New Jersey, USA