title: Homology modeling of T. cruzi and L. major NADH-dependent fumarate reductases: ligand docking, molecular dynamics validation, and insights on their binding modes.
abstract: Leishmania major and Trypanosoma cruzi are the main causes of leishmaniasis and Chagas disease, two endemic parasitosis identified as neglected diseases by the World Health Organization. Fumarate reductase (FR) is a central enzyme in the conversion of fumarate to succinate, an energy releasing path essential for the survival of these protozoans which is also absent in their mammalian hosts. FR can thus be considered as a good candidate for targeting specific inhibition by new drugs designed against L. major and T. cruzi. The lack of tertiary structures available for LmFR and TcFR has limited until now the possibility of performing structure-based drug design. Here we used homology modeling combined with enzyme-cofactor docking to propose tertiary structures for NADH-dependent LmFR and TcFR using an homologous X-ray crystallographic structure of flavine-adenine dinucleotide (FAD) dependent FR from Shewanella frigidimarina (PDB ID: 1QO8) as template. These models were refined and stabilized with/without substrate in the active site using classical molecular dynamics simulations under quasi-physiological conditions. Structural features relevant for understanding the mechanism of action of the enzyme were also analyzed, with special attention to the hydrogen bond network involving the cofactor and water molecules present at the binding sites. A small set of compounds previously synthesized and assayed for their inhibitory capacity against TcFR ([M(mpo)₂] metal complexes with M=Pt(II), Pd(II) and V(IV)O and mpo=2-mercaptopyridine N-oxide) and LmFR (licochalcone A) were screened by protein-ligand docking using the NADH-LmFR and NADH-TcFR models here proposed and validated, gaining insight into their binding modes in each enzyme.
authors.affiliation: Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay. Electronic address: amerlino@fcien.edu.uy.
authors.forename: Alicia
authors.initials: A
authors.lastname: Merlino
authors.affiliation: Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, C. C. 1157, 11800 Montevideo, Uruguay.
authors.forename: Marisol
authors.initials: M
authors.lastname: Vieites
authors.affiliation: Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, C. C. 1157, 11800 Montevideo, Uruguay.
authors.forename: Dinorah
authors.initials: D
authors.lastname: Gambino
authors.affiliation: Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay. Electronic address: laurac@fcien.edu.uy.
authors.forename: E Laura
authors.initials: EL
authors.lastname: Coitiño
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D017124:Conserved Sequence; D005650:Fumarates / Q000737:chemistry; D006860:Hydrogen Bonding; D018320:Leishmania major / Q000201:enzymology*; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D009243:NAD / Q000737:chemistry; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D015800:Protozoan Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein; D013385:Succinate Dehydrogenase / Q000737:chemistry*; D019802:Succinic Acid / Q000737:chemistry; D014349:Trypanosoma cruzi / Q000201:enzymology*
chemical_list: D005650:Fumarates; D015800:Protozoan Proteins; D009243:NAD; C032005:fumaric acid; D019802:Succinic Acid; D044925:Oxidoreductases Acting on CH-CH Group Donors; C020155:fumarate reductase (NADH); D013385:Succinate Dehydrogenase
keywords: Anti-trypanosomatids rational design; Computational modeling; NADH-dependent fumarate reductase 3D structure; NADH/fumarate binding mode; Trypanosoma cruzi/Leishmania major fumarate reductases inhibitors