crenolanib Imidazo purine diones were another cluster
1-Imidazo[2,1-]purine-2,4(3,8)-diones were another cluster of compounds identified from the Chembridge screen (). A benzyl group at the R2 position was preferred over a phenyl or 2-phenylpropyl (. and ), and -substitution of the benzyl group increased potency to the nanomolar level ( IC=0.20μM . ). A methyl group at the R1 position led to a slight increase in potency (. and . ), and removal of the aromatic moiety at R2 did not cause a major impact on enzymatic inhibition, indicating the importance of the heterocyclic core in the binding event ( vs. ). The R3 position tolerated substituents such as methoxyethyl or alkyl, but the unsubstituted analogue provided the best profile (. ). The low calculated LogP in this crenolanib chemical series translated to very good LLE (∼5) for the two most active compounds, and good LE (0.3–0.5) (c). Fused polyaromatic systems are known DNA intercalators, and caution should be exercised when using this class of compounds in cellular experiments.
The 5-[1,3,4]thiadiazolo[3,2-]pyrimidin-5-one and 5-thiazolo[3,2-]pyrimidin-5-one hits, illustrated by the general formula depicted in , were characterised by a hetero-bicyclic core substituted with an amide or a reversed amide at the R3 position, and lipophilic substituents at the R1 and/or R2 positions. For the thiadiazolopyrimidinone hits, R1 was not present, and in the case of R2, an alkyl chain was preferred over a methyl or methoxymethyl ( and . and ). A -chlorine substituent on the phenyl amide chain was preferred to - or -methyl groups ( and . ). For thiazolopyrimidinone hits, removal of the R1 and R2 substituents abolished enzymatic activity (), and in accordance with the thiadiazolopyrimidinone SAR, an -substituent on the phenyl amide chain was preferred to -substituent (. ). A reversed amide was an acceptable R3 replacement, but only when a methylated benzylic position was present (. ). Active compounds in this series presented an encouraging LE and LLE balance (d), deeming them as worthy starting points towards hit optimisation, and as indicated by the SAR, possibly with room for increased Fsp3 (f).
During the CBCS screening campaign, we identified the series of bi-cyclic compounds summarised in . Isoxazolo[4,5-]pyridin-4(5)-one was the most common core in this class, but isoxazolo[4,5-]pyrimidin-4(5)-one and furo[3,2-]pyridin-4(5)-ones were present too. The phenyl ring was substituted at R3 with a nitrogen-containing group, such as dimethylamine (), succinimide (), pyrrolidine (), morpholine () or piperazine (), to give single-digit micromolar or sub-micromolar IC values. Larger substituents, such as 4-benzylpiperidinyl () or a benzyloxy group (), or removal of the R3 group, were not tolerable structural modifications ( and ). The R4 position was generally a methyl group, but it could also accommodate a benzyl group (. ), and the R1 position accepted aromatic substituents, such as phenyl ( and ) or pyridyl ( and ). Isoxazolo[4,5-]pyrimidin-4(5)-one examples containing active structural motifs, such as aryl R1 and amine R3, also displayed inhibitory activity ( and ), with the chloro-phenyl derivative being the most potent inhibitor in this class (IC=0.28µM). A furo[3,2-]pyridin-4(5)-one core with an aryl ring at the R2 position instead of the R1, was completely inactive (. ), and highlighted the importance of this region of the scaffold. Despite the sub-par LE and LLE, when compared with other series (e), the aliphatic amine group present in this series, increased the Fsp3 (f), and could provide a handle to improve aqueous solubility during hit optimisation.
Introduction Deamination of cytidine nucleotides to uridine nucleotides is essential for conversion to thymidine nucleotides. However, uracil-containing intermediates can be mutagenic or cytotoxic. Deoxyuridine 5′-triphosphate nucleotidohydrolases (dUTPases) play an essential role in the nucleotide metabolism of all organisms by catalyzing the hydrolysis of dUTP to dUMP+pyrophosphate (Ppi).1., 2. This provides dUMP, a precursor for dTTP synthesis by thymidylate synthase, and protects DNA from misincorporation of dUTP in place of dTTP by lowering dUTP:dTTP ratios. Uridine nucleotides can also arise in DNA through the spontaneous deamination of cytidine, which accounts for a significant percentage of DNA base damage. If left unrepaired, uracil can create CG to TA transition mutations. When uracil is found in DNA, either from misincorporation instead of thymine or spontaneous deamination of cytosine, the base excision repair pathway is initiated by uracil DNA glycosylase (UDG), which recognizes a U:A mispair but which can result in apyrimidinic sites or DNA strand cleavage if the damage is not properly processed. To adjust levels of dCTP in relation to dTTP in the nucleotide pool, dCTP can be converted to dUTP in archaea and some bacteria by dCTP deaminase, then acted upon by dUTPase to form dUMP. dUMP is subsequently converted to dTTP by thymidylate synthase and thymidylate kinase. Eukaryotes and some bacteria create dUMP directly from dCMP via a zinc-dependent dCMP deaminase.6., 7.