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

Abstract

Background(-)-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.ResultsWe 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′′O2H) groups on the benzophenone moiety, when bound to PKCε as well as PKA.ConclusionsTo 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.Electronic supplementary materialThe online version of this article (10.1186/s12859-017-1955-7) contains supplementary material, which is available to authorized users.

3-Deoxy-2β,16-dihydroxynagilactone E, a natural compound from Podocarpus nagi, preferentially inhibits JAK2/STAT3 signaling by allosterically interacting with the regulatory domain of JAK2 and induces apoptosis of cancer cells

“…This mechanism of B6 is novel and different from those of many other known tyrosine kinase inhibitors, which interact with the ATP-binding pockets of JAKs. Because the ATP-binding pockets of kinases are highly conserved, it is therefore difficult to obtain compounds that specifically interact with a particular ATP-binding pocket [ 43 , 44 ]. Future JAK2 inhibitors that target similar sites via allosteric mechanisms may provide alternative therapeutic strategies to inhibit specific JAK/STAT pathways.…”

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε

“…We adapted the charge state validation workflow as described previously [ 49 ]. Briefly, initial charge state of 1c in each ATP site of nPKC isozyme refers to our previous work [ 49 ], that the amine (N1) on the azepane ring, the phenolic group (C6′′OH), and the carboxylate (C15′′O 2 H) on the benzophenone moiety bear charges. value was computed from each trajectory of nPKC-bound 1c .…”

Exploring the Potency of <i>Nigella sativa</i> Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations

“…The protonation state of a chemical structure, which is contributed by any titratable functional group, depends on environmental pH [24]. Meanwhile, the correct assignment of protonation state has a crucial role in producing meaningful studies of molecular docking [31] and dynamics simulation [24]. Thus, we predicted charge states of secondary metabolites in N. sativa seeds at physiological pH (7.4) using MarvinView 18.21.0.…”

“…Hence, another method, such as molecular dynamics (MD) simulation, should be implemented after the molecular docking step to obtain a more accurate prediction of energy and conformation. MD simulations have been employed in many studies of protein-ligand interactions [23][24][25].…”