Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases

• Published in: BMC bioinformatics Vol. 18; no. Suppl 16; p. 572
• Main Authors: Hardianto, Ari, Yusuf, Muhammad, Liu, Fei, Ranganathan, Shoba
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 28-12-2017; BioMed Central; BMC
• Subjects: Acids - chemistry; Adenosine Triphosphate - metabolism; ATP mimic; Azepines - chemistry; Azepines - pharmacology; Cancer; Care and treatment; Cyclic adenylic acid; Cyclic AMP-Dependent Protein Kinases - antagonists & inhibitors; Cyclic AMP-Dependent Protein Kinases - metabolism; Fluorides; Fluorine - chemistry; Force and energy; Humans; Hydroxybenzoates - chemistry; Hydroxybenzoates - pharmacology; Isoenzymes; Isoenzymes - chemistry; Isoenzymes - metabolism; Kinase inhibitors; Kinetics; Ligand charge state; Ligands; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; Protein Kinase C - antagonists & inhibitors; Protein Kinase C - metabolism; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Protein kinases; Static Electricity; Structural Homology, Protein; Ligand charge state; ATP mimic; Molecular modelling; Molecular dynamics simulation; Kinase inhibitors
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-017-1955-7

(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications.
We explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6''OH) and the carboxylate (C15''O
H) groups on the benzophenone moiety, when bound to PKCε as well as PKA.
To the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.