Discovery and Structure–Activity-Relationship Study of N-Alkyl-5-hydroxypyrimidinone Carboxamides as Novel Antitubercular Agents Targeting Decaprenylphosphoryl-β-d-ribose 2′-Oxidase

Abstract

Magnesium plays an important role in infection with Mycobacterium tuberculosis (Mtb) as a signal of the extracellular environment, as a cofactor for many enzymes, and as a structural element in important macromolecules. Raltegravir, an antiretroviral drug that inhibits HIV-1 integrase is known to derive its potency from selective sequestration of active-site magnesium ions in addition to binding to a hydrophobic pocket. In order to determine if essential Mtb-related phosphoryl transfers could be disrupted in a similar manner, a directed screen of known molecules with integrase inhibitor-like pharmacophores (N-alkyl-5-hydroxypyrimidinone carboxamides) was performed. Initial hits afforded compounds with low-micromolar potency against Mtb, acceptable cytotoxicity and PK characteristics, and robust SAR. Elucidation of the target of these compounds revealed that they lacked magnesium dependence and instead disappointingly inhibited a known promiscuous target in Mtb, decaprenylphosphoryl-β-d-ribose 2′-oxidase (DprE1, Rv3790).

Promiscuous Targets for Antitubercular Drug Discovery: The Paradigm of DprE1 and MmpL3

“…Promiscuous targets could be an obstacle in the discovery of novel antitubercular drug targets, being recurrently found in HTS [110], nevertheless, they have been proven really useful for the development of novel drug candidates. This is well demonstrated by the fact that five compounds currently in clinical trials inhibit these targets, with DprE1 inhibitors TBA-7379, BTZ043 and Macozinone in Phase I, while the QcrB inhibitor Telacebec, the MmpL3 inhibitor SQ109 and again the Macozinone are in Phase II [26][27][28][29].…”

Tuberculosis Drug Discovery: A Decade of Hit Assessment for Defined Targets

“…Importantly, an 8-fold enhancement in activity was obtained by replacing a m-Me with a trifluoromethyl group in C, suggesting that the m-CF 3 was making important contacts to DprE1 active site residues. Replacement of the phenyl with a pyridine moiety in C in (Naik et al, 2014) 1.2 Pyrazolopyridones N/D (Panda et al, 2014) 1.3 2-Carboxy quinoxalines N/D (Neres et al, 2015) 1.4 5-Hydroxy pyrimidinediones N/D (Oh et al, 2018) 2.1 MmpL3 Adamantyl ureas N/D (Brown et al, 2011;North et al, 2013) 2.2 Indolecarboxamides Yes b (Onajole et al, 2013;Stec et al, 2016) 2.3 Yes b (Kondreddi et al, 2013) 2.4 Tetrahydropyrazolo pyrimidine carboxamide…”

“…The pyrimidinedione scaffold was identified by HTS of a library from St. Jude Children’s Research Hospital comprised of 6,207 molecules containing the pyrimidinedione substructure. The rationale for screening against pyrimidinediones was based on the favorable druglike properties of this scaffold which is found in a variety of FDA approved drugs including Raltegravir, many of which have been found to inhibit Mg 2+ -dependent enzymes based on their Mg 2+ chelation within the active site of their targets ( Oh et al., 2018 ). The N -alkyl-5-hydroxypyrimidinone carboxamide hit 6 ( Table 1 ) was selected based on its more favorable physicochemical properties but no evidence of Mg 2+ -dependence was found with the resistance conferring mutations mapping to dprE1 which was further confirmed by DprE1 under-expression studies.…”

Biological Profiling Enables Rapid Mechanistic Classification of Phenotypic Screening Hits and Identification of KatG Activation-Dependent Pyridine Carboxamide Prodrugs With Activity Against Mycobacterium tuberculosis

“…Resistance to one of these compounds, TCA1, maps to Y314C (Wang et al, 2013), a mutation which causes a structural change in the enzyme active site (Liu et al, 2017). Resistance to N-alkyl-5hydroxypyrimidinone carboxamides was associated with the amino acid substitutions Y314C, Y314H, and P116S in DprE1 (Oh et al, 2018). Likewise, the G253E mutation in MmpL3 has been implicated in resistance to a wide range of MmpL3 inhibitors which include the tetrahydropyrazolopyrimidine THPP1, the 1,2-diamine SQ109, the adamantyl urea, AU1235, the indolecarboxamides NITD-304 and NITD-349 (Li et al, 2019), and other diverse inhibitors (Williams et al, 2019).…”