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

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AbstractBackground 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 2 f, 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 2 f 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. General Significance The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.

Authors: Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

HITS at TAC KBP 2015: Entity discovery and linking, and event nugget detection

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Authors: Benjamin Heinzerling, Alex Judea, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Incremental global event extraction

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Authors: Alex Judea, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Lexical coherence graph modeling using word embeddings

Abstract

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Authors: Mohsen Mesgar, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Search space pruning: A simple solution for better coreference resolvers

Abstract

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Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Which coreference evaluation metric do you trust? A proposal for a link-based entity aware metric

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Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Generating coherent summaries of scientific articles using coherence patterns

Abstract

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Authors: Daraksha Parveen, Mohsen Mesgar, Michael Strube

Date Published: 2016

Publication Type: InProceedings

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