Dynamics of CYP51: implications for function and inhibitor design

Abstract

Sterol 14α-demethylase (cytochrome P450 family 51 (CYP51)) is an essential enzyme occurring in all biological kingdoms. In eukaryotes, it is located in the membrane of the endoplasmic reticulum. Selective inhibitors of trypanosomal CYP51s that do not affect the human CYP51 have been discovered in vitro and found to cure acute and chronic mouse Chagas disease without severe side effects in vivo. Crystal structures indicate that CYP51 may be more rigid than most CYPs, and it has been proposed that this property may facilitate antiparasitic drug design. Therefore, to investigate the dynamics of trypanosomal CYP51, we built a model of membrane-bound Trypanosoma brucei CYP51 and then performed molecular dynamics simulations of T. brucei CYP51 in membrane-bound and soluble forms. We compared the dynamics of T. brucei CYP51 with those of human CYP51, CYP2C9, and CYP2E1. In the simulations, the CYP51s display low mobility in the buried active site although overall mobility is similar in all the CYPs studied. The simulations suggest that in CYP51, pathway 2f serves as the major ligand access tunnel, and both pathways 2f (leading to membrane) and S (leading to solvent) can serve as ligand egress tunnels. Compared with the other CYPs, the residues at the entrance of the ligand access tunnels in CYP51 have higher mobility that may be necessary to facilitate the passage of its large sterol ligands. The water (W) tunnel is accessible to solvent during most of the simulations of CYP51, but its width is affected by the conformations of the heme's two propionate groups. These differ from those observed in the other CYPs studied because of differences in their hydrogen-bonding network. Our simulations give insights into the dynamics of CYP51 that complement the available experimental data and have implications for drug design against CYP51 enzymes.

Trypanosoma brucei CYP51: Essentiality and Targeting Therapy in an Experimental Model

“…Additional research should be performed to determine potential combinations with other drugs currently under investigation in HAT such as fexinidazole [84,85] or oxaboroles [86]. Further research should also be conducted to identify new molecules that target more specifically trypanosome CYP51 with enhanced affinity to the enzyme in order to improve the efficiency in combination [87]. …”

The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

“…dmd.aspetjournals.org models of P450s. Since then, many independent models of membrane anchored P450s have been published, so we can discuss common features and differences among individual P450 forms (Denisov et al, 2012;Sgrignani and Magistrato, 2012;Baylon et al, 2013;Berka et al, 2013;Ghosh and Ray, 2013;Yu et al, 2015).…”

Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design

“…However, distinct features of CYP51 compared to other CYPs have been observed in experiments and in molecular dynamics (MD) simulations. These features include high substrate specificity, binding site rigidity, different open tunnels between the active site and the protein surface, and plasticity of the two heme propionate groups [1,8,9]. Because of CYP51's potential as a target for anti-parasitic drug design, it is important to study these features of CYP51.…”

“…We have previously built and simulated a model of membrane-bound T. brucei CYP51 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer based on a crystal structure of the globular domain of T. brucei CYP51 [8]. The mapping of ligand tunnels that have been found in other CYPs to the model of the membrane-bound T. brucei CYP51 are, according to Wade's nomenclature [10]: tunnel 2a (between the F-G loop, B-B’ loop and β1-1 sheet) and tunnel 2 f (between the A’ and F” helices and the tip of the β4 hairpin) which lead to the membrane, and tunnels 1 (between the C, D, H and L helices), 2b (between the B-B’ loop and the β1-2 and β1-4 sheets), 2c (between the G and I helices and the B’-C loop), 2 ac (between the B’ helix and G helix), 2e (through the B-C loop), S (the solvent tunnel, between the F and I helices and the β4 hairpin) and W (the water tunnel, between the C helix, the B-B’ loop and helix K” of the heme bulge segment) which lead to the solvent (Figs.…”