| Literature DB >> 34066895 |
Kamran Waidha1, Nikhil Ponnoor Anto2, Divya Ram Jayaram2, Avi Golan-Goldhirsh3, Saravanakumar Rajendran4, Etta Livneh2, Jacob Gopas2,5.
Abstract
Water lily (Nuphar) bioactive extracts have been widely used in traditional medicine owing to their multiple applications against human ailments. Phyto-active Nuphar extracts and their purified and synthetic derivatives have attracted the attention of ethnobotanists and biochemists. Here, we report that 6,6'-dihydroxythiobinupharidine (DTBN), purified from extracts of Nuphar lutea (L.) Sm. leaves, is an effective inhibitor of the kinase activity of members of the protein kinase C (PKC) family using in vitro and in silico approaches. We demonstrate that members of the conventional subfamily of PKCs, PKCα and PKCγ, were more sensitive to DTBN inhibition as compared to novel or atypical PKCs. Molecular docking analysis demonstrated the interaction of DTBN, with the kinase domain of PKCs depicting the best affinity towards conventional PKCs, in accordance with our in vitro kinase activity data. The current study reveals novel targets for DTBN activity, functioning as an inhibitor for PKCs kinase activity. Thus, this and other data indicate that DTBN modulates key cellular signal transduction pathways relevant to disease biology, including cancer.Entities:
Keywords: 6,6′-dihydroxythiobinupharidine (DTBN); Nuphar lutea; Ramachandran plot; homology docking modeling; kinase inhibitor; protein kinase C (PKC)
Year: 2021 PMID: 34066895 PMCID: PMC8125885 DOI: 10.3390/molecules26092785
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
Figure 1DTBN downregulates PKC catalytic activity in a concentration-dependent manner. In vitro kinase assays of indicated PKC isoforms were performed, as described in Materials and Methods, utilizing MBP as a substrate. Before the initiation of the assay, DTBN was added to the samples at several concentrations. Following the termination of the assay, sample proteins were then resolved by SDS-PAGE and developed by autoradiography (a). p32-MBP and MBP protein band signals were quantified using Image Lab software, and the relative amounts of p32-MBP/MBP were presented in a line graph (b). Immunoblotting against HA and MBP to detect overexpressed PKC expression, and MBP, respectively, monitor equal loading of samples. Data are representative of two independent experiments. Molecular weight markers (in kDa) are indicated on the left, and arrows mark the positions of the indicated protein bands. IgH, Ig heavy chain.
Inhibition of PKC isoforms by DTBN.
| PKC Isoforms | IC50 Values (μg/mL) | IC50 Values (μM) |
|---|---|---|
| PKCα | 0.092 | 0.174 |
| PKCγ | 0.089 | 0.168 |
| PKCε | 7.5 | 14.23 |
| PKCη | >10 | >19 |
| PKCζ | 9.8 | 18.6 |
| PKCδ | >10 | >19 |
Results of molecular docking.
| PKC Isoforms | ΔG Bind * (Kcal/mol) of DTBN | Control Molecule | ΔG Bind * (Kcal/mol) |
|---|---|---|---|
| PKCα | −40.83 | NVP-AEB071 | −71.92 |
| PKCγ | −30.74 | GO6983 | −57.18 |
| PKCε | −23.25 | NVP-AEB071 | −44.22 |
| PKCη | −20.73 | 2,6-Naphthyridine | −56.52 |
| PKCζ | −19.61 | - | - |
| PKCδ | −19.0 | NVP-AEB071 | −61.35 |
* post mm-GBSA refinement.
Figure 2ATP binding kinase domain site alignment and invariant lysine residue of PKC isoforms. Red: Denotes variation in the ATP binding site residue of PKCζ (GRGSYA: Gly264 into Ala264, Phe263 into Tyr263, and Lys260 into Arg260). Yellow: Conserved Glycine Rich region of ATP Binding site across PKC isoforms, Green: Invariant Lysine Residue across PKC isoforms which structures the enzyme for phosphoryl-transfer. * Denotes position which has fully conserved amino acid residues across multiple sequences. “:” Denotes conservation between groups of strong similar properties. “.” Denotes conservation between groups of weakly similar properties.
Figure 3DTBN at PKCα binding pocket (a) 3D image and (b) 2D image.
Interaction of DTBN in binding pocket of different PKC isoforms.
| PKC Isoforms | H-Bond Interaction | π···π and π···S Interaction |
|---|---|---|
|
| (i) −NH hydrogen of Asn421 and furan ring −O of DTBN (N−H···O, 2.91 Å) | π···π interaction between phenyl and furan ring of Tyr419 and DTBN, respectively (2.24 Å) |
|
| carboxylic oxygen (−OH) of Asp441 and hydrogen of −OH proximal to the thiophene sulfur in DTBN (O−H···O, 2.41 Å) | π···π interaction between phenyl and furan ring of Phe362 and DTBN (4.80 Å). |
|
| (i) side-chain carboxylic oxygen (C=O) of Asp536 and hydrogen of −OH group proximal to thiophene sulphur in DTBN (O−H···O, 1.91 Å) | π···π interaction between phenyl and furan ring of Phe419 and DTBN, respectively (4.90 Å). |
|
| carboxylic oxygen (−OH) of Asp440 and carboxylic oxygen (C=O) of Asp483 involved in hydrogen bond with −OH group proximal to thiophene sulphur in DTBN (two O−H···H, 2.31 and 2.88 Å, respectively) | (i) π···S interaction between phenyl and thiophene sulphur of |
|
| (i) side-chain hydroxy oxygen of Ser262 and carboxylic oxygen (−OH) of Asp380 involved in hydrogen bond with −OH groups of DTBN (two O−H···O, 1.98 and 1.96 Å, respectively) | - |
|
| - | - |
Figure 4DTBN at PKCγ binding pocket (a) 3D image and (b) 2D image.
Figure 5DTBN at PKCε binding pocket (a) 3D image and (b) 2D image.
Figure 6DTBN at PKCη binding pocket (a) 3D image and (b) 2D image.
Figure 7DTBN at PKCδ (top) and PKCζ (bottom) binding pockets (a) and (c) 3D images, and (b,d) 2D images.
Figure 8Comparison of DTBN in the binding pocket of PKCα (left) and PKCδ (right).
Homology models properties.
| Protein Model | Template | Seq. Identity | Seq. | Coverage | GQME | Qmean | Range |
|---|---|---|---|---|---|---|---|
|
| 3IW4.1.A | 76.99% | 0.55 | 0.49 | 0.35 | −1.78 | 345–686 |
|
| 5f9e.1.A | 72.99% | 0.53 | 0.49 | 0.32 | −0.41 | 343–674 |
|
| 3txo.1.A | 72.02% | 0.53 | 0.46 | 0.32 | −0.32 | 406–733 |
|
| 5li1.1.A | 84.15% | 0.57 | 0.59 | 0.39 | −0.63 | 246–585 |
Homology models structure assessment.
| Protein Model | MolProbity Score | Ramachandran Favoured | Ramachandran Outliner | ERRAT Overall Quality Factor | ProSA |
|---|---|---|---|---|---|
|
| 1.94 | 93.53% | 0.59% | 93.91 | −8.0 |
|
| 1.08 | 96.97% | 0.00% | 89.35 | −8.59 |
|
| 1.31 | 96.32% | 0.61% | 88.56 | −8.06 |
|
| 0.87 | 97.93% | 0.30% | 92.76 | −9.73 |
Figure 9Ramachandran plot of (a) PKCγ and (b) PKCε.
Figure 10Ramachandran plot of (a) PKCδ and (b) PKCζ.
The site-score and residues involved in the ATP Binding Pocket of PKC isoforms.
| PKC Isoforms | Site Score | Predicted Site Amino Acid Residue Numbers |
|---|---|---|
|
| 1.042 | 357,358,361,362,365,378,380,399,403,418,434,435,436,437,438,439,440,444,445,448,482,484,485,487,490,497,498,499,631,633,634,635,636,638, 639 |
|
| 1.078 | 414,415,418,419,422,435,437,456,460,470,486,487,488,489,492,493,495,496,499,532,534,536,537,539,549,550,551,552,553,697,698,699,702 |
|
| 1.044 | 258,259,260,261,262,263,264,266,279,281,314,330,331,332,333,337,339,340,343,376,378,380,381,383,393,394,396,397,414,548,549,551 |
|
| 1.037 | 355,356,358,359,360,361,362,363,376,378,379,380,381,384,385,388,390,392,393,394,396,397,399,401,411,422,427,428,429,430,434,436,437,440,471,472,473,475,477,478,480,490,491,492,493,494,495,496,497,498,507,633,634,637,644,645,646 |