Pyrimidin-2(1H)-ones based inhibitors of Mycobacterium tuberculosis orotate phosphoribosyltransferase

• Published in: European journal of medicinal chemistry 2012-08, Vol.54, p.113-122
• Main Authors: Breda, Ardala, Machado, Pablo, Rosado, Leonardo Astolfi, Souto, André Arigony, Santos, Diógenes Santiago, Basso, Luiz Augusto
• Format: Article
• Language: English
• Subjects: Anti-Bacterial Agents - chemical synthesis; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; Biological and medical sciences; Inhibitors; Medical sciences; Miscellaneous; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - enzymology; Orotate phosphoribosyltransferase; Orotate Phosphoribosyltransferase - antagonists & inhibitors; Orotate Phosphoribosyltransferase - metabolism; Pharmacology. Drug treatments; Pyrimidin-2(1H)-ones compounds; Pyrimidine; Pyrimidinones - chemical synthesis; Pyrimidinones - chemistry; Pyrimidinones - metabolism; Pyrimidinones - pharmacology; Time Factors; Tuberculosis
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2012.04.031

Tuberculosis (TB) is an ancient human chronic infectious disease caused mainly by Mycobacterium tuberculosis. The emergence of strains resistant to first and second line anti-TB drugs, associated with the increasing number of TB cases among HIV positive subjects, and the large number of individuals infected with latent bacilli have urged the development of new strategies to treat TB. Enzymes of nucleotide metabolism pathways provide promising molecular targets for the development of drugs, aiming at both active and latent TB. The orotate phosphoribosyltransferase (OPRT) enzyme catalyzes the synthesis of orotidine 5′-monophosphate from 5′-phospho-α-d-ribose 1′-diphosphate and orotic acid, in the de novo pyrimidine synthesis pathway. Based on the kinetic mechanism and molecular properties, here we describe the design, selection and synthesis of substrate analogs with inhibitory activity of M. tuberculosis OPRT (MtOPRT) enzyme. Steady-state kinetic measurements were employed to determine the mode of inhibition of commercially available and chemically derived compounds. The 6-Hydroxy-2-oxo-1,2-dihydropyridine-4-carboxylic acid (6) chemical compound and its derivative, 3-Benzylidene-2,6-dioxo-1,2,3,6-tetrahydropyridine-4-carboxylic acid (13), showed enzyme inhibition constants in the submicromolar range. Isothermal titration calorimetry data indicated that binding of both compounds to MtOPRT have negative enthalpy and favorable Gibbs free energy probably due to their high complementarity to the enzyme's binding pocket. Improvement of compound 13 hydrophobic character by addition of an aromatic ring substituent resulted in entropic optimization, reflected on a thermodynamic discrimination profile characteristic of high affinity ligands. These inhibitors represent lead compounds for further development of MtOPRT inhibitors with increased potency, which may be tested as anti-TB agents. [Display omitted] ► Selection and optimization of inhibitors based on MtOPRT kinetic mechanism. ► Identification of MtOPRT inhibitors with nanomolar inhibition constant values. ► In vitro kinetic assays to characterize binding mode of inhibitors. ► Thermodynamic discrimination profiles of inhibitors assessed by ITC. ► Inhibitory activity of 13 is likely due to entropy optimization.