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. 2019 Nov 15;9(11):740.
doi: 10.3390/biom9110740.

Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood

Abheepsa Mishra  1   2 , Satyahari Dey  1
Affiliations

Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood

Abheepsa Mishra et al. Biomolecules. .

Abstract

Natural products from plants, such as chemopreventive agents, attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure-based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide-based therapeutics have been developed to combat several health disorders, including cancers, metabolic disorders, heart-related diseases, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, the in silico activities of cyclic peptides towards molecular targets, such as protein kinases, proteases, and apoptosis related proteins have not been extensively investigated. In this study, we explored the in silico kinase and protease inhibitor potentials of cyclosaplin, and studied the interactions of cyclosaplin with other apoptosis-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that were used in the current study as well. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 kcal/mol indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB, and p38, indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis-related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein-ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands, especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave the insights of cyclosaplin being a potential apoptosis inducer and protein kinase inhibitor.

Keywords: apoptosis; cyclosaplin; molecular docking; protein kinases; sandalwood.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The different peptide-based ligands for targeting cancer-related proteins used in docking studies. Cyan blue = carbon, grey = hydrogen, deep blue = nitrogen, red = oxygen, and yellow = sulfur.
Figure 2
Figure 2
(a) Possible targets of cyclosaplin as predicted by Swiss Target Prediction. (b) Different energy minimized proteins (rainbow spectrum) used in docking studies. (A) EGFR kinase. (B) VEGFR2 kinase. (C) PKB. (D) p38. (E) PTEN. (F) MMP-2. (G) MMP-9. (H) Procaspase 3. (I) Procaspase 7. (J) Caspase 9. (K) TRAIL. (L) SURVIVIN.
Figure 3
Figure 3
(a) Docking scores in kcal/mol for various cancer-related proteins. The binding affinities closer to 10 indicate efficient binding. (b) Cyclosaplin bound to different receptors. Cyclosaplin is shown in white, indicated by the arrows, and proteins are depicted with rainbow’s spectrum. (A) EGFR kinase. (B) VEGFR2 kinase. (C) PKB. (D) p38. (E) PTEN. (F) MMP-2. (G) MMP-9. (H) Procaspase 3 (previous study [11]). (I) Procaspase 7. (J) Caspase 9. (K) TRAIL. (L) SURVIVIN.
Figure 4
Figure 4
Peptide based ligands bound to specific proteins. Ligands are shown in white, indicated by the arrows, and proteins are depicted in rainbow spectrum. (A) CVRACGAD bound to EGFR kinase, (B) Cilengitide bound to VEGFR2 kinase, (C) RPRTSSF bound to PKB, (D) FWCS bound to p38, (E) YSV bound to PTEN, (F) CTTHWGFTLC bound to MMP-2, (G) CRRHWGFEFC bound to MMP-9, (H) Cilengitide bound to Procaspase 3, (I) RGDS bound to Procaspase 7, (J) RGDS bound to Caspase 9, (K) CKVILTHRC unbound to TRAIL, and (L) AYACNTSTL bound to SURVIVIN.
Figure 5
Figure 5
Interaction of cyclosaplin with various cancer-related proteins. (A) EGFR Kinase. (B) VEGFR2 Kinase. (C) PKB. (D) p38. (E) PTEN. (F) MMP-2. (G) Procaspase 3. (H) Procaspase 7. (I) Caspase 9. (J) SURVIVIN.
Figure 6
Figure 6
Protein–ligand interactions using LigPlot. (A) CVRACGAD and EGFR kinase. (B) Cilengitide and VEGFR2 kinase. (C) RPRTSSF and PKB. (D) FWCS and p38. (E) YSV and PTEN. (F) CTTHWGFTLC and MMP-2. (G) Cilengitide and Procaspase 3. (H) RGDS and Procaspase 7. (I) RGDS and Caspase 9. (J) AYACNTSTL and SURVIVIN.
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