Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.
BACKGROUND
Cytochrome P450 sterol 14α-demethylase (CYP51) is an essential enzyme for sterol biosynthesis and a target for anti-parasitic drug design. However, the design of parasite-specific drugs that inhibit parasitic CYP51 without severe side effects remains challenging. The active site of CYP51 is situated in the interior of the protein. Here, we characterize the potential ligand egress routes and mechanisms in Trypanosoma brucei and human CYP51 enzymes.


METHODS
We performed Random Acceleration Molecular Dynamics simulations of the egress of four different ligands from the active site of models of soluble and membrane-bound T. brucei CYP51 and of soluble human CYP51.


RESULTS
In the simulations, tunnel 2f, which leads to the membrane, was found to be the predominant ligand egress tunnel for all the ligands studied. Tunnels S, 1 and W, which lead to the cytosol, were also used in T. brucei CYP51, whereas tunnel 1 was the only other tunnel used significantly in human CYP51. The common tunnels found previously in other CYPs were barely used. The ligand egress times were shorter for human than T. brucei CYP51, suggesting lower barriers to ligand passage. Two gating residues, F105 and M460, in T. brucei CYP51 that modulate the opening of tunnels 2f and S were identified.


CONCLUSIONS
Although the main egress tunnel was the same, differences in the tunnel-lining residues, ligand passage and tunnel usage were found between T. brucei and human CYP51s.


CONCLUSIONS
The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Xiaofeng
X
Yu
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Prajwal
P
Nandekar
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Ghulam
G
Mustafa
Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
Vlad
V
Cojocaru
Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN, USA.
Galina I
GI
Lepesheva
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany. Electronic address: rebecca.wade@h-its.org.
Rebecca C
RC
Wade
D001665:Binding Sites; D015195:Drug Design; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D058886:Sterol 14-Demethylase / Q000737:chemistry*; D014346:Trypanosoma brucei brucei / Q000187:drug effects*
D008024:Ligands; D058886:Sterol 14-Demethylase
CYP51; Cytochrome P450; Ligand access and egress; Membrane-bound protein; Random acceleration molecular dynamics; Sterol 14α-demethylase