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Molecular Static and Dynamic Analyses Reveal Flaw in
Murine Model used by US FDA to Detect Drug Carcinogenicity
Molecular Static and Dynamic Analyses Reveal Flaw in
Murine Model used by US FDA to Detect Drug Carcinogenicity
Trevor G Marshall, Autoimmunity Research Foundation, CA, USA and Murdoch University, Western Australia
The US FDA currently accepts carcinogenicity studies of
pharmaceutical drugs based on murine models. In addition to 6 month
studies with p53(+/-) and ras.H2 transgenic mice, lifetime studies
(typically 2 years) in WT mice or rats are also considered as evidence
that a drug lacks carcinogenic activity. This model is not always
exhaustive. For example, during the acceptance testing of the ARB
Olmesartan[1], possible carcinogenicity observed in hamsters was not
able to be duplicated in rats, or in transgenic mice. We have previously
used the static molecular modeling of AutoDock to demonstrate that
Olmesartan has agonostic activity in the PDB:1DB1 model of the
human VDR Nuclear Receptor[2], while it has antagonistic activity in
the PDB:1RK3 model of the rat VDR. This agonism has now been
confirmed with Molecular Dynamics, using GROMACS. The murine
VDR indeed lost its ability to bind the DRIP 205 co activator when
Olmesartan was the ligand, while the human VDR was activated by
Olmesartan similarly to its native ligand (1,25-dihydroxyvitamin-D).
Since the VDR is believed to express 913 genes[3], many of which are
known to be associated with cancer pathogenesis, good homology
between human VDR, and the animal model VDR, is exceedingly
important.
CONCLUSION: The murine environment is inadequate to accurately
model drug carcinogenic activity in humans. A species should be
chosen which has a VDR LBP homology closer to that of man. AutoDock
and GROMACS molecular analyses are useful in resolving any
remaining anomalies in the observed data.
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Plots of inter-molecular atomic contacts make it easy to see that 1,25-
dihydroxyvitamin-D binds symmetrically into the VDR from both
Homo sapiens and Rattus norvegicus, yet the conformation of chemical
ligands is different, due to lack of VDR homology.
References:
1. FDA CDER: NDA-21-286, Sankyo Pharma Inc Available from URL
http://www.fda.gov/cder/foi/nda/2002/21-286_Benicar.htm
2. Marshall TG: VDR Nuclear Receptor Competence is the Key to Recovery from
Chronic Inflammatory and Autoimmune Disease.
Abstract presentation, DMM2006.
3. Wang TT, et al: Large-scale in silico and microarray-based identification of
direct 1,25-dihydroxyvitamin-D3 target genes.
Mol Endoctrinol. 2005 Nov;19(11):2685-95.
This video was created using the GROMACS Molecular
Dynamics software on a small computing cluster assembled
from PCs based on Core-2-duo CPU technologies. The
difference in steady-state ligand conformation between
human and rat VDR can clearly be seen at
http://autoimmunityresearch.org/dmm2007/dmm2007.ram
Nature Precedings : doi:10.1038/npre.2007.52.1 : Posted 15 Jun 2007
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Plots of the instantaneous number of hydrogen bonds
compiled during the molecular dynamics simulations
show surprising similarities, and differences, between
the behavior of the Olmesartan-VDR complexes.
Analysis of the rat VDR and DRIP205 model (PDB:1RK3)
show that the activation of the VDR is only partly due to
the AF-2 domain. There are hbonds from GLU416 to
DRIP MET629/LEU630, but there are also hbonds from
LYS260 to HIS627, and LYS242 to LEU633.
Human
Rat
Four hydrogen bonds
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Nature Precedings : doi:10.1038/npre.2007.52.1 : Posted 15 Jun 2007