Chapter I. Synthesis, modification and bioactivity of bicyclic thieno[3,2-D]pyrimidines

1.1.24Synthesis of Disubstituted Analogues of the Thienopyrimidinone Core

Reagents and conditions: (a) 4-fluorobenzaldehyde, AcOH, MW, 180 °C, 4 h, 22%, (b) phosphorus oxychloride, reflux, 18 h, 72%; (c) morpholine, DMF, MW, 150 °C, 1 h, 32%.
The SAR data gathered during hit identification and hit-to-lead exploratory medicinal chemistry revealed key pharmacophore features of thienopyrimidinone series that contributed to their potency against clinical strains of C. difficile. These observations included the following: (a) the nitrophenyl portion of the hit 2 from the initial screening can be replaced with isosteric nitrothienyl and nitrofuranyl to enhance potency in a ligand-efficient manner (6a−6c), (b) the C2- methyl substitution does not significantly influence potency (6d−6f), (c) the presence of an electronwithdrawing regiospecific nitro group on a bicyclic scaffold is indispensable to the potency of these compounds (7a vs 6a, 7b vs 6b, and 7c vs 6c), (d) the C2-methyl can be extended to an aryl/heteroaryl styrene moiety without significant loss of potency (e) the N3-position of thienopyrimidinone scaffold can be substituted with various arylalkyl moieties, aliphatic esters, or aliphatic amides with retention of potency; however, direct aromatic ring attachment led to a noticeable loss of potency, (f) the C4 carbonyl oxygen can be replaced with chloro and aromatic/aliphatic amines with retention of activity (g) either C2-, N3- or C2-, C4-disubstitutions on pyrimidine ring of 6a proved detrimental and (h) compounds with the carboxylic acid substituent showed detrimental activities. The most promising compound (8f) from this series exhibited an excellent profile: (i) potent and rapid killing effect against C. difficile strains, (ii) excellent selectivity over human normal microflora, (iii) low cytotoxicity against mammalian cells, (iv) increased GI stability, and (v) desirable aqueous solubility. Unlike synthetically intractable and architecturally complex macrocyclic antibiotics, vancomycin (MW = 1449 Da) and fidaxomicin (MW = 1058 Da) that are difficult to structurally optimize, the current series of small MW thienopyrimidinones offer significant scope for further medicinal chemistry optimization to explore SAR and improve in vitro activity without increasing the molecular size and complexity beyond 600 Da[70].