Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors

Abstract

Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were identified. The structural basis for the binding affinity and selectivity was determined by analysis of a three-dimensional crystal structure of a CDK2-inhibitor complex. The cellular effects of these compounds were characterized in mammalian cells and yeast. In the latter case the effects were characterized on a genome-wide scale by monitoring changes in messenger RNA levels in treated cells with high-density oligonucleotide probe arrays. Purine libraries could provide useful tools for analyzing a variety of signaling and regulatory pathways and may lead to the development of new therapeutics.

Cellular effects of purvalanol A: A specific inhibitor of cyclin‐dependent kinase activities

“…5) and in the MCF-7 cells (data not shown). As cdk4 is not efficiently inhibited by purvalanol A in cell-free conditions (EC 50 850 nM), 17 these observations suggest that this compound interfered with the activation of the cdk4/cyclin D1 complex. A possible mechanism could rely on an increase of the expression of a cdki protein.…”

“…16,17 This compound showed virtually no effect with the numerous non-cdk protein kinases tested, and had little overall effect on the contents of most cellular mRNAs. Our preliminary experiments indicated that it was active in several established cell lines at moderate concentrations (10 M), in contrast with other cdk inhibitors (olomoucine, roscovitine, butyrolactone).…”

A small molecule based on the pRb2/p130 spacer domain leads to inhibition of cdk2 activity, cell cycle arrest and tumor growth reduction in vivo

“…Therefore, targeting cdk activity has become an attractive strategy in cancer therapy, as it could potentially create a rationally designed inhibitor of a specific process that leads a cell to malignant transformation. To date, several families of chemical inhibitors targeted against different cdk activities have been described (Losiewicz et al, 1994;Gray et al, 1998) and, for some of them, their anticancer therapeutic potential has been demonstrated in preclinical studies (Dai and Grant, 2004). Recent attention has been focused on biological molecules, rather than chemotherapeutic agents, that combine the effectiveness of arresting cellular growth through interaction with important cell cycle checkpoint regulators, and the low risk of unexpected adverse reactions, thus improving clinical safety and patient tolerability.…”

N‐(Indazolyl)benzamido Derivatives as CDK1 Inhibitors: Design, Synthesis, Biological Activity, and Molecular Docking Studies

“…The most important CDK2 / purvanalol A-simulated close contacts involve residues Ile10, Gly11, Gly13, Ala31, Val64, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Lys89, Asn132, Leu134, Ala144, Asp145, HOH5, and HOH96 while, in a similar way, CDK2-actives-simulated close contacts involve residue Ile10, Gly11, Val18, Ala31, Val64, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Leu134, HOH5, and HOH96. As can be seen in Fig.5, according to literature data [6], purvanalol A forms a complete triplet of hydrogen bonds between the N7-imidazole nitrogen and the backbone nitrogen of Leu83 (distance = 2.20 ), the N6-amino group and the backbone oxygen of Leu83 (distance = 2.42 ), and the acidic C8 atom of the purine ring and the backbone oxygen of Glu81 (distance = 2.72 ). Compound 9m, forms only a pair of bidentate hydrogen bonds between the N2-indazole nitrogen and the backbone nitrogen of Leu83 (distance = 2.17 ) and N1 indazole nitrogen and the backbone oxygen of Glu81 (distance = 2.45 ); the same intermolecular hydrogen bonds of 9m were observed for all the other most active N-(indazolyl)benzamides 9e, f, i, l, n.…”

“…In particular, olomoucine 1 [4], roscovitine 2 [5], purvalanol A 3 [6], O 6 -cyclohexylmethylguanine (NU2058) 4, and its analoge NU61025 [7] are significant examples of such kind of molecules ( Fig. 1).…”