Conformationally Constrained Analogues of Diacylglycerol (DAG). 16. How Much Structural Complexity Is Necessary for Recognition and High Binding Affinity to Protein Kinase C?

• Published in: Journal of medicinal chemistry 2000-03, Vol.43 (5), p.921-944
• Main Authors: Nacro, Kassoum, Bienfait, Bruno, Lee, Jeewoo, Han, Kee-Chung, Kang, Ji-Hye, Benzaria, Samira, Lewin, Nancy E, Bhattacharyya, Dipak K, Blumberg, Peter M, Marquez, Victor E
• Format: Article
• Language: English
• Subjects: 4-Butyrolactone - analogs & derivatives; 4-Butyrolactone - chemical synthesis; 4-Butyrolactone - chemistry; 4-Butyrolactone - metabolism; 4-Butyrolactone - pharmacology; Antineoplastic Agents - chemical synthesis; Antineoplastic Agents - chemistry; Antineoplastic Agents - metabolism; Antineoplastic Agents - pharmacology; Binding, Competitive; Biological and medical sciences; Crystallography, X-Ray; Drug Design; Drug Screening Assays, Antitumor; Enzyme Activation; Epidermal Growth Factor - antagonists & inhibitors; Epidermal Growth Factor - metabolism; Isoenzymes - chemistry; Isoenzymes - metabolism; Ligands; Medical sciences; Miscellaneous; Models, Molecular; Pharmacology. Drug treatments; Protein Kinase C - chemistry; Protein Kinase C - metabolism; Protein Kinase C-alpha; Stereoisomerism; Structure-Activity Relationship; Tumor Cells, Cultured; Valerates - chemical synthesis; Valerates - chemistry; Valerates - metabolism; Valerates - pharmacology
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm9904607

The design of potent protein kinase C (PK-C) ligands with low nanomolar binding affinities was accomplished by the combined use of pharmacophore- and receptor-guided approaches based on the structure of the physiological enzyme activator, diacylglycerol (DAG). Earlier use of the former approach, which was based on the structural equivalence of DAG and phorbol ester pharmacophores, identified a fixed template for the construction of a semirigid “recognition domain” that contained the three principal pharmacophores of DAG constrained into a lactone ring (DAG-lactones). In the present work, the pharmacophore-guided approach was refined to a higher level based on the X-ray structure of the C1b domain of PK-Cδ complexed with phorbol-13-O-acetate. A systematic search that involved modifying the DAG-lactone template with a combination of linear or branched acyl and α-alkylidene chains, which functioned as variable hydrophobic “affinity domains”, helped identify compounds that optimized hydrophobic contacts with a group of conserved hydrophobic amino acids located on the top half of the C1 domain where the phorbol binds. The hydrophilic/hydrophobic balance of the molecules was estimated by the octanol/water partition coefficients (log P) calculated according to a fragment-based approach. The presence of branched α-alkylidene or acyl chains was of critical importance to reach low nanomolar binding affinities for PK-C. These branched chains appear to facilitate important van der Waals contacts with hydrophobic segments of the protein and help promote the activation of PK-C through critical membrane interactions. Molecular modeling of these DAG-lactones into an empty C1b domain using the program AutoDock 2.4 suggests the existence of competing binding modes (sn-1 and sn-2) depending on which carbonyl is directly involved in binding to the protein. Inhibition of epidermal growth factor (EGF) binding, an indirect PK-C mediated response, was realized with some DAG-lactones at a dose 10-fold higher than with the standard phorbol-12,13-dibutyrate (PDBU). Through the National Cancer Institute (NCI) 60-cell line in vitro screen, DAG-lactone 31 was identified as a very selective and potent antitumor agent. The NCI's computerized, pattern-recognition program COMPARE, which analyzes the degree of similarity of mean-graph profiles produced by the screen, corroborated our principles of drug design by matching the profile of compound 31 with that of the non-tumor-promoting antitu