Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex

<div><p>Flavonoids, a class of natural compounds with variable phenolic structures, have been found to possess anti-cancer activities by modulating different enzymes and receptors like CDK6. To understand the binding behavior of flavonoids that inhibit the active CDK6, molecular dynamics (MD) simulations were performed on six inhibitors, chrysin (M01), fisetin (M03), galangin (M04), genistein (M05), quercetin (M06) and kaempferol (M07), complexed with CDK6/cyclin D. For all six flavonoids, the 3’-OH and 4’-OH of B-ring were found to be favorable for hydrogen bond formation, but the 3-OH on the C-ring and 5-OH on the A-ring were unfavorable, which were confirmed by the MD simulation results of the test molecule, 3’, 4’, 7-trihydroxyflavone (M15). The binding efficiencies of flavonoids against the CDK6/cyclin D complex were mainly through the electrostatic (especially the H-bond force) and vdW interactions with residues ILE19, VAL27, ALA41, GLU61, PHE98, GLN103, ASP163 and LEU152. The order of binding affinities of these flavonoids toward the CDK6/cyclin D was M03 > M01 > M07 > M15 > M06 > M05 > M04. It is anticipated that the binding features of flavonoid inhibitors studied in the present work may provide valuable insights for the development of CDK6 inhibitors.</p></div

Average MM-PBSA free energies (kcal/mol) of flavonoid-CDK6/cyclin D complexes.

<p>Average MM-PBSA free energies (kcal/mol) of flavonoid-CDK6/cyclin D complexes.</p

Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex - Fig 6

<p>(a) Chemical structure of M15; (b) RMSD profile of M15-CDK6/cyclin D complex; (c) M15-CDK6/cyclin D interaction plot; (d) The number of hydrogen bonds during the MD simulation.</p

Model of crosstalk between MLK3 and AMPK in stress responses.

<p>Model of crosstalk between MLK3 and AMPK in stress responses.</p

The weak interaction analysis in flavonoid-CDK6/cyclin D complex.

<p>The weak interaction analysis in flavonoid-CDK6/cyclin D complex.</p

<i>Per</i> residue decomposition energies (Δ<i>G</i>bind^residue) of crucial amino acids in various inhibitors.

<p><i>Per</i> residue decomposition energies (Δ<i>G</i>bind^residue) of crucial amino acids in various inhibitors.</p

MLK3 phophorylated AMPKα at T172.

<p>A: HEK293 cells were transfected with empty control, MLK3 or LKB1 vectors. Total proteins were extracted for immunoblotting of pAMPKα-T172 and AMPKα. B: Recombinant AMPK and MLK3 were respectively expressed in HEK293T cells and purified by GSH. <i>In vitro</i> kinase assays were performed as indicated in the presence or absence of AMP. The phosphorylation of AMPK at T172 was determined by western blot analysis.</p

The molecular docking results of flavonoids.

<p>The molecular docking results of flavonoids.</p

Average MM-PBSA free energies (kcal/mol) of flavonoid-CDK6/cyclin D complexes.

<p>Average MM-PBSA free energies (kcal/mol) of flavonoid-CDK6/cyclin D complexes.</p

Flavonoid-CDK6/cyclin D interaction plots generated by LigPlot+[46] and the stereo view of flavonoid-CDK6/cyclin D interaction.

<p>Flavonoid-CDK6/cyclin D interaction plots generated by LigPlot+[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196651#pone.0196651.ref046" target="_blank">46</a>] and the stereo view of flavonoid-CDK6/cyclin D interaction.</p