Fragment-Based Discovery of 7-Azabenzimidazoles as Potent, Highly Selective, and Orally Active CDK4/6 Inhibitors

Abstract

Herein, we describe the discovery of potent and highly selective inhibitors of both CDK4 and CDK6 via structure-guided optimization of a fragment-based screening hit. CDK6 X-ray crystallography and pharmacokinetic data steered efforts in identifying compound 6, which showed >1000-fold selectivity for CDK4 over CDKs 1 and 2 in an enzymatic assay. Furthermore, 6 demonstrated in vivo inhibition of pRb-phosphorylation and oral efficacy in a Jeko-1 mouse xenograft model.

Targeting CDK6 in cancer: State of the art and new insights

“…Moreover, phosphorylation of Thr172 in the T-loop does not result in the activation of the enzyme bound to cyclin D1. Furthermore, there are several 3.10 1JOW CDK6 -Vcyclin -9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido [4,5]pyrrolo[1,2-d]pyrimidin-2-amine 109 2.90 4TTH CDK6 -Vcyclin -Aminopurvalanol 114 2.80 2F2C CDK6 -Vcyclin -Fisetin 117 2.90 1XO2 CDK6 -Vcyclin -PD0332991 114 3.00 2EUF CDK6 -Kcyclin -p18 INK4c 118 2 111 2.70 4EZ5 CDK6 -1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone 111 2.31 4AUA CDK6 -4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine 119 2.60 3NUP CDK6 -4-[5-chloro-3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(5-piperazin-1-ylpyridin-2-yl)pyrimidin-2-amine 119 2.70 3NUX CDK6 -p16 INK4a 83 3.40 1BI7 CDK6 -p19 INK4d 74,83 1.90 1BLX 2.80 1BI8 lines of evidence showing that CDK4 might not even be phosphorylated by CAK. 77,78 The INK4 family of CDK inhibitors (CDKIs) which include p16 INK4a , p15 INK4b , p18 INK4c , and p19 INK4d are specific to CDK4 and CDK6.…”

“…92,107,108 In addition to the above clinical experimental drug compounds, a few pre-clinical CDK4/6 inhibitors, i.e., 7X, AMG925, Compound 6, Compound A and PD0183812, have been reported. [109][110][111][112][113] The chemical structures and CDK inhibitory activity of these compounds are summarized in Table 3. A close examination of the chemical structures of PD0332991, LEE011, LY2835219, AMG925 and Compound A reveals a general N-NH-N sequence of the pyrimidine-amine-pyridine or pyrazineamine-thiazole system.…”

“…For example, pyridine in AMG 925 has been shown to form an edge to face aromaticaromatic contact with the gatekeeper residue Phe98. 109,111 Docking and scoring of 7X (Table 3), which is highly structurally similar to PD0332991, have identified a binding orientation different from that of PD0332991. This has been attributed to the rigidity and higher electron withdrawing effect of the cyano group when compared with the acetyl group.…”

Fragment-Based Approaches to the Discovery of Kinase Inhibitors

“…An example of this has been published recently (Cho et al, 2012). However, these findings mirror our own experience, where we have frequently taken an unselective fragment hit and (via careful structure-guided optimization) produced a highly selective lead compound, even against closely related targets.…”

“…A wide variety of screening methodologies have been used, including X-ray screening (Betzi et al, 2011;Cho et al, 2012;Howard et al, 2009;Schulz et al, 2011;Wyatt et al, 2008), HCS (Hughes et al, 2011;Iwata et al, 2012;Li et al, 2012;Matthews et al, 2009;Medina et al, 2010), surface plasmon resonance (SPR) (Soth et al, 2011;Xiang et al, 2011), NMR spectroscopy ( Jahnke et al, 2010;Johnson et al, 2011;Lee et al, 2012;Ray et al, 2011), virtual screening (Giordanetto, Kull, & Dellsén, 2011;Moffett et al, 2011), and even de novo design (Charrier et al, 2011). A wide variety of screening methodologies have been used, including X-ray screening (Betzi et al, 2011;Cho et al, 2012;Howard et al, 2009;Schulz et al, 2011;Wyatt et al, 2008), HCS (Hughes et al, 2011;Iwata et al, 2012;Li et al, 2012;Matthews et al, 2009;Medina et al, 2010), surface plasmon resonance (SPR) (Soth et al, 2011;Xiang et al, 2011), NMR spectroscopy ( Jahnke et al, 2010;Johnson et al, 2011;Lee et al, 2012;Ray et al, 2011), virtual screening (Giordanetto, Kull, & Dellsén, 2011;Moffett et al, 2011), and even de novo design (Charrier et al, 2011).…”