Structures of purine nucleosidase fromTrypanosoma bruceibound to isozyme-specific trypanocidals and a novel metalorganic inhibitor

Abstract

Sleeping sickness is a deadly disease that primarily affects sub-Saharan Africa and is caused by protozoan parasites of the Trypanosoma genus. Trypanosomes are purine auxotrophs and their uptake pathway has long been appreciated as an attractive target for drug design. Recently, one tight-binding competitive inhibitor of the trypanosomal purine-specific nucleoside hydrolase (IAGNH) showed remarkable trypanocidal activity in a murine model of infection. Here, the enzymatic characterization of T. brucei brucei IAGNH is presented, together with its high-resolution structures in the unliganded form and in complexes with different inhibitors, including the trypanocidal compound UAMC-00363. A description of the crucial contacts that account for the high-affinity inhibition of IAGNH by iminoribitol-based compounds is provided and the molecular mechanism underlying the conformational change necessary for enzymatic catalysis is identified. It is demonstrated for the first time that metalorganic complexes can compete for binding at the active site of nucleoside hydrolase enzymes, mimicking the positively charged transition state of the enzymatic reaction. Moreover, we show that divalent metal ions can act as noncompetitive IAGNH inhibitors, stabilizing a nonproductive conformation of the catalytic loop. These results open a path for rational improvement of the potency and the selectivity of existing compounds and suggest new scaffolds that may be used as blueprints for the design of novel antitrypanosomal compounds.

In Silico Investigation of Flavonoids as Potential Trypanosomal Nucleoside Hydrolase Inhibitors

“…The crystal structure of T. b. brucei IAG-NH (PDB ID: 4I71) resolved at 1.28 Å [ 15 ] and T. b. brucei IG-NH (PDB ID: 3FZ0) [ 30 ] were retrieved from the Protein Data Bank [ 31 ]. Both structures had cocrystallized ligands.…”

“…The 3D structures of the ligands are downloaded from PubChem. The selected binding sites for both enzymes were the ones reportedly occupied by the inhibitors AGV and BTB in the crystal structures [ 15 , 30 ]. Controlled docking was performed with ligands AGV and BTB and two of the natural substrates, guanosine and inosine, for validation of the experimental protocol.…”

“…The reaction can be simplified as follows: where the nucleoside can be inosine, guanosine, and/or adenosine depending on its specific preference of substrates. Two types of NH have been reported for T. brucei , the purine nucleoside specific inosine-adenosine-guanosine nucleoside hydrolase (IAG-NH) and the 6-oxopurine-specific inosine-guanosine nucleoside hydrolase (IG-NH) [ 14 , 15 ]. Inhibition of NH depletes the level of purine bases in T. brucei , retarding their growth and multiplication.…”

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases—Part III: In-Silico Molecular Docking Investigations

“…1LDG [147]; 1CEQ, 1CET [148]; 1T24, 1T25, 1T26, 1T2C, 1T2D [149]; 1U4O, 1U4S, 1U5A, 1U5C, 1XIV [150]; 2A94 [151]; 4B7U [152] Lipoamide dehydrogenase (LADH) 2QAE [153] Lysyl-tRNA synthetase (Lys-RS) 4H02 [154] M1 amino peptidase (A-M1) 4K5L, 4K5M, 4K5N, 4K5O, 4K5P [155] M17 amino peptidase (A-M17) 4K3N [155]; 3KQX, 3KQZ, 3KR4, 3KR5 [156]; 3T8V, 3T8W [157] M18 aspartyl aminopeptidase (M18AAP) 4EME [158] Macrophage infectivity potentiator (MIP) 1JVW [159] Metacaspase-2 (MCA2) 4AF8, 4AFP, 4AFV [160] Metallocarboxypeptidase 1 (MCP-1) 3DWC [161] Methionine aminopeptidase 1b (MAP1b) 3S6B [162] 4A26 [167] Nicotinamidase (PnC1) 3R2J [168] N-Myristoyl transferase (NMT) 2WUU [169] 3H5Z, 2WSA [170]; 4A2Z, 4A30, 4A31, 4A32, 4A33 [171] Nucleoside 2-deoxyribosyltransferase (NDRT) 2A0K, 2F2T, 2F62, 2F64, 2F67 [172] Nucleoside diphosphate kinase B (NDKB) 3NGR, 3NGS, 3NGT, 3NGU [173] 4FKX, 4FKY [174]; 4F4A, 4F36 [175] 3NGR, 3NGS, NGT, 3NGU, 3PRV [173] Nucleoside hydrolase (NH) 1EZR [176] Inosine-Adenosine-Guanosine nucleoside hydrolase (IAGNH) 4I70, 4I71, 4I72, 4I73, 4I74, 4I75 [177] Inosine-Guanosine nucleoside hydrolase (IG-NH) 3FZ0, 4I70, 4I71, 4I72, 4I73, 4I74, 4I75 [178] Nucleosome assembly protein (NapL) 3FS3 [179]; 3GYV, 3GYW [180] Old yellow enzyme (OYE) 3ATY, 3ATZ [181]; 4E2B, 4E2D [182] Oligopeptidase B (OPB) 2XE4 [183] 4BP8, 4BP9 [184] Ornithine decarboxylase (ODC) 1QU4 …”

Immucillins Impair Leishmania (L.) infantum chagasi and Leishmania (L.) amazonensis Multiplication In Vitro

“…In order to establish a successful infection, Leishmania and other protozoa parasites have developed efficient mechanisms for rapid synthesis of DNA and replication. Protozoa parasites including Leishmania [ 12 , 13 ], Plasmodium [ 14 , 15 ], Entamoeba histolytica [ 16 , 17 ], Giardia lamblia [ 18 ], Toxoplasma gondii [ 19 , 20 ] Trypanosoma [ 21 , 22 ] and a few bacteria and fungi [ 23 ] are purine auxotrophs, that obtain their purines from exogenous precursors through purine salvage pathways [ 24 ]. In cells, nucleosides are hydrolyzed by nucleoside hydrolases (NH) [ 13 ] or undergo phosphorolysis by purine nucleoside phosphorylase (PNP) which release the purine bases to be used in parasite DNA synthesis [ 24 ].…”