In order to shed light on the potential mode ofaction of chalcones, and to understand why some chalcones inhibiteither NF-κB or HDACs and some inhibit both, we have carried outmolecular modeling, molecular similarity and docking studies. Thecompounds were docked into the binding sites of HDAC8, and the beststudied HDAC enzyme was selected based on the position of theco-crystalized ligand in the crystal structure of the complex (pdbentries 1T69 and 3ETZ) (). TheGlideScore values were compared to the activities that wereexperimentally obtained (). The results of the docking indicated that all chalconescould favorably bind in the active site, although not all moleculesshowed activity. The most active molecule 12 had a less favorableGlideScore than chalcone 21 that exhibited the most favorablebinding. The binding mode of these two molecules is different() which may be the result ofthe large active site of HDAC8 which accommodates two(4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide)moieties in the interior pocket of the protein. Furthermore, thedocking could not distinguish the third active molecule 10 from therest of the group. There is a clear difference between theGlideScore of the binding of 21 to 20. However, 20 binds almost asgood as 12 and better than 10, resulting in the absence of thecorrelation between activity and binding affinity determined byGlide. We hypothesize that molecules that are not active couldpossibly bind preferably elsewhere on the protein surface ratherthan on the active site.
The effect of chalcone derivatives (nos. 1–21) wasexamined on total HDAC activity using a fluorescence HDAC assay. Asshown in , four chalconeaglycones, namely isoliquiritigenin (no. 10), butein (no. 12),homobutein (no. 15) and the glycoside marein (no. 21), reduced HDACactivity in a concentration-dependent manner (ICvalues 60–190 μM, ). Butein(no. 12) appeared to be the best inhibitor of HDAC activity. Otherchalcone derivatives were assumed as inactive, because they wereunable to provide distinct inhibitory effect even at the highesttest concentration (1000 μM).
Some of the compounds tested herein have previouslybeen reported as NF-κB inhibitors including isoliquiritigenin (no.10) () and butein (no. 12)(). We have previouslydemonstrated that 4′-hydroxychalcone showed 26S protease inhibitionactivity on three different proteolytic activities (chymotrypsin,trypsin- and caspase-like) in a dose-dependent manner (). The involvement of natural chalconesin cancer tumorigenesis has been reviewed (). To the best of our knowledge this isthe first study aiming to screen a natural chalcone library andattempting to draw SARs among them. Several natural chalconesemerged as relatively good inhibitors of NF-κB. Additionally, HDACwas identified as a novel potential target for the chalconesdescribed.
The list and values of descriptors, observed andcalculated are shown in .The statistics indicate reasonable descriptive value of the modelthat shows which molecular properties influence activity of themolecules in the NF-κB assay. Since we could not develop asatisfactory model that would differentiate the active and inactivemolecules, we examined the molecular similarity and differencesbetween most active molecules and the inactive ones. Conformationalsearch carried out by Omega software and the Merck Molecular ForceField force revealed that all molecules can exist in severaldifferent conformations due to the free rotation around bondsbetween carbonyl carbon and neighboring groups. ROCS search andcomparison of electrostatic forces showed that unsurprisinglymolecules are similar (Shape Tanimoto coefficients are between 0.94and 0.0.69 and Tverstsky coefficients are between 0.91 and 0.71).The highest similarity was observed between the most activechalcone molecule 13 and inactive 9, indicating that shape andelectrostatic properties are not sufficient to explain thedifferent activities of the group.
Srinivasan B, Johnson TE, Lad R and XingC: Structure-activity relationship studies of chalcone leading to3-hydroxy-4,3′,4′,5′-tetramethoxychalcone and its analogues aspotent nuclear factor kappaB inhibitors and their anticanceractivities. J Med Chem. 52:7228–7235. 2009.
Chalcones (1,3-diphenyl-2-propenones) are a group ofaromatic compounds that represent a large class of natural productsfound in many medicinal plants, fruits, vegetables, spices andnuts. They are the natural precursors of flavonoids and display avariety of biological activities. Although the modes of action ofthis class of compounds are not fully understood, great efforts aredevoted to elucidate the mechanisms underlying their promisinganti-inflammatory and anticancer activities. Hence several naturalchalcones have been reported to inhibit the NF-κB signaling, andnumerous synthetic derivatives have been evaluated instructure-activity relationship (SAR) studies (,).Besides the NF-κB inhibition, interference in microtubule formationis generally thought to be responsible for their anticanceractivities (,). Despite the cross-talk and modulationeffects between NF-κB and HDACs, and structural similarity ofchalcones to broad-spectrum HDAC inhibitors SAHA and trichostatinA, HDACs have not been investigated as potential targets fornatural chalcones. In this study, we aimed to test twenty-onecommercially available chalcones () for dual HDACs and NF-κB inhibitory activities . Viability assays were also carried out to elucidate thecytotoxic potential of the chalcones against leukemia cells. Wealso aimed to explore SAR to determine the essentialfunctionalities on the chalcone core for biological activity. Wealso performed molecular modeling and docking studies in an attemptto understand the potential mode and mode/site of binding ofnatural chalcones to NF-κB and class I type HDACs.
In the present study, several reaction steps have been carried out to synthesize three sub classes of flavonoids namely; chalcones, dihydrochalcones and flavanones with various substituents attached.
The 2D structures of chalcone molecules were drawnusing SketchEI and transferred into the VEGA ZZ molecular modelingsoftware (,) to generate 3D structures. Allmolecules were saved into a single mol file, that was used as inputfor the OMEGA, OpenEye Scientific Software (Omega version 2.3.2;) to generate a maximum of2 low energy conformers with default values. These conformationswere stored as OEB file extension format and their 3D similaritywas compared using the Rocs, OpenEye Scientific Software (Rocsversion 2.3.1; ). E-DragonSoftware () was utilized tocalculate constitutional and molecular property descriptors. Thedescriptors selected to describe the SAR were selected usingPartial Least Squares regression as implemented in the PLSR moduleof Virtual Computational Chemistry Laboratory () and Gretl software was used tocalculate the correlation between the logarithm of the activity andpredicted molecular properties.
Best binding poses of chalcone 12(thick stick representation) and chalcone 21 (thin stickrepresentation) within the active site of the HDAC8 represented bysurface only. The docking was carried out using Glide and DSVisualizer 3.1 was used to prepare the image.
Yadav VR, Prasad S, Sung B and AggarwalBB: The role of chalcones in suppression of NF-kappaB-mediatedinflammation and cancer. Int Immunopharmacol. 11:295–309. 2011. : :
Orlikova B, Tasdemir D, Golais F, Dicato Mand Diederich M: Dietary chalcones with chemopreventive andchemotherapeutic potential. Genes Nutr. 6:125–147. 2011. : :