| Literature DB >> 29081608 |
Eram Shakeel1,2, Salman Akhtar1,2, Mohd Kalim Ahmad Khan1,2, Mohtashim Lohani3, Jamal M Arif1,3, Mohd Haris Siddiqui1,2.
Abstract
Survivin (IAP proteins) remains an important target for anticancer drug development as it is reported to be over-expressed in tumor cells to enhance resistance to apoptotic stimuli. The study focuses on virtual screening of marine compounds inhibiting survivin, a multifunctional protein, using a computational approach. Structures of compounds were prepared using ChemDraw Ultra 10. Software and converted into its 3D PDB structure and its energy was minimized using Discovery Studio client 2.5. The target protein, survivin was retrieved from RCSB PDB. Lipinski's rule and ADMET toxicity profiling was carried out on marine compounds and the filtered compounds were further promoted for molecular docking analysis and interaction studies using AutoDock Tools 4.0. Molecular docking results revealed that analog (AP 4) of Aplysin, showed very promising inhibitory potential against survivin with a binding energy of -8.75 kcal/mol and Ki 388.28 nM as compared to its known inhibitor, Celecoxib having binding energy of -6.65 kcal/mol and Ki 13.43 μM. AP 4. The analog depicted similarity in pattern when compared to standard. The result proposes AP 4, is an effective molecule exhibiting prominent potential to inhibit survivin and thus promoting apoptosis in tumor cells.Entities:
Keywords: Aplysin; Apoptosis; Marine; Survivin; analogs
Year: 2017 PMID: 29081608 PMCID: PMC5651222 DOI: 10.6026/97320630013293
Source DB: PubMed Journal: Bioinformation ISSN: 0973-2063
Figure 1Mechanism of Survivin Pathway: Overexpression of survivin promotes tumor cell survival through (i) inactivation of Apaf-1, Casapase 9, Mdm-2, p53 (ii) causes uncontrolled mitosis in tumor cells through Cdk1 (iii) promotes angiogenesis through activation of Vascular endothelial growth factor (VEGF).
Pharmacokinetic parameters for the measurement of drug concentrations in blood or plasma.
| S. No | ADME Properties | Activity range |
| 1 | Human intestinal absorption (HIA) absorption | Poorly- 0~20% |
| Moderate- 20~70% | ||
| High- 70~100% | ||
| 2 | Blood brain barrier (BBB) | CNS active compounds (+); >1 |
| CNS inactive compounds (-); < 1 | ||
| 3 | Plasma protein Binding (% PBP) | Chemicals strongly bound > 90% |
| Chemicals weakly bound < 90% | ||
| 4 | Madin-Darby canine kidney (MDCK) cell permeability | Lower- < 25 |
| Moderate- 25~500 | ||
| Higher- > 500 | ||
| 5 | Heterogenous human epithelial colorectal adenocarcinoma (Caco2) cell permeability | Lower- < 4 |
| Moderate- 4~70 | ||
| Higher- < 70 |
ADMET profiling of novel marine Analogs with their parent compound
| S.No. | Analogs | BBB | Caco2 | PPB | HIA | SP | Toxicity (M/C) |
| Celecoxib | 0.0272 | 0.499 | 91.07 | 96.68 | 91.07 | +/-- | |
| Aplysin | 6.3979 | 55.769 | 91.48 | 100 | -1.153 | +/-- | |
| 1 | AP1 | 6.051 | 56.37 | 91.07 | 100 | -1.271 | +/-- |
| 2 | AP4 | 0.501 | 52.898 | 86.22 | 97.655 | -2.474 | -/-- |
| 3 | AP10 | 1.011 | 0.532 | 93.37 | 94.491 | -3.052 | +/-- |
| 4 | AP11 | 0.991 | 32.419 | 100 | 99.408 | -2.078 | +/-- |
| 5 | AP12 | 4.6 | 57.01 | 85.24 | 100 | -2.639 | +/-- |
| 6 | AP13 | 9.444 | 56.814 | 85.24 | 100 | -2.792 | +/-- |
| 7 | AP14 | 1.506 | 56.068 | 96.39 | 100 | -3.507 | +/-- |
| 8 | AP15 | 5.003 | 52.956 | 82.44 | 98.35 | -3.599 | +/-- |
| 9 | AP16 | 0.286 | 57.61 | 96.85 | 99.244 | -1.145 | -/-- |
| 10 | AP18 | 2.141 | 57.95 | 99.511 | 99.234 | -1.164 | +/-- |
| 11 | AP20 | 2.033 | 57.16 | 93.35 | 98.525 | -1.918 | -/-- |
| 12 | AP21 | 1.581 | 55.904 | 91.66 | 98.117 | -3.054 | -/-- |
| 13 | AP23 | 2.628 | 57.71 | 99.22 | 99.218 | -1.214 | -/-- |
| 14 | AP24 | 4.643 | 57.697 | 93.2 | 98.742 | -1.647 | -/-- |
| 15 | AP26 | 3.423 | 55.039 | 93.84 | 97.302 | -3.07 | -/-- |
| 16 | AP28 | 12.66 | 57.359 | 88.5 | 99.202 | -0.847 | -/-- |
| 17 | AP29 | 0.259 | 2.304 | 94.56 | 97.193 | -2.791 | +/-- |
| 18 | AP36 | 1.15793 | 50.0446 | 75.56 | 93.456 | -3.9018 | -/-- |
| 19 | AP37 | 3.85254 | 47.4872 | 98.36 | 97.4917 | -2.313 | -/-- |
| 20 | AP40 | 1.7326 | 56.98 | 97.58 | 98.244 | -2.604 | +/-- |
| 21 | AP43 | 3.77079 | 1.58846 | 90.23 | 98.54 | -1.006 | +/-- |
| 22 | AP47 | 1.24665 | 57.5445 | 97.25 | 98.08 | -1.438 | +/-- |
| Abbreviations: BBB- Blood brain barrier; HIA-Human intestinal absorption; SP-Skin permeability; MDCK- Madin-Darby canine kidney; Caco-2- heterogenous human epithelial colorectal adenocarcinoma; M- mutagen; C-carcinogen(rat, mouse) | |||||||
Structure of designed novel analogs
| S.No. | Analogs | R1 |
| 1. | AP 1 | - |
| 2. | AP 4 | - |
| 3. | AP 10 | Cl |
| 4. | AP 11 | - |
| 5. | AP 12 | Cl |
| 6. | AP 13 | Br |
| 7. | AP 14 | Br |
| 8. | AP 15 | Br |
| 9. | AP 16 | - |
| 10. | AP 18 | - |
| 11. | AP 20 | - |
| 12. | AP 21 | - |
| 13. | AP 23 | - |
| 14. | AP 24 | - |
| 15. | AP 26 | - |
| 16. | AP 28 | - |
| 17. | AP 29 | - |
| 18. | AP 36 | - |
| 19. | AP 37 | - |
| 20. | AP 40 | - |
| 21. | AP 43 | - |
| 22. | AP 47 | - |
Novel Analogs following Drug-Likeliness Test along with the standard drug
| S. no | Analogs | Mol.Wt | NoN | NoHNH | Log P |
| Celecoxib | 381.373 | 3.4 | 1 | 7 | |
| Aplysin | 295.22 | 1 | 0 | 5.15 | |
| 1 | AP 1 | 236.74 | 1 | 0 | 4.26 |
| 2 | AP 2 | 251.76 | 2 | 2 | 4.05 |
| 3 | AP 3 | 284.32 | 1 | 0 | 5.25 |
| 4 | AP 4 | 266.77 | 2 | 0 | 4.62 |
| 5 | AP 5 | 265.78 | 2 | 1 | 4.42 |
| 6 | AP 6 | 251.76 | 2 | 2 | 4.15 |
| 7 | AP 7 | 253.73 | 3 | 3 | 2.76 |
| 8 | AP 8 | 331.82 | 2 | 2 | 5.63 |
| 9 | AP 9 | 350.26 | 1 | 1 | 6.53 |
| 10 | AP 10 | 335.26 | 4 | 3 | 3.07 |
| 11 | AP 11 | 477.85 | 2 | 0 | 6.77 |
| 12 | AP 12 | 319.88 | 2 | 0 | 4.77 |
| 13 | AP 13 | 384.75 | 2 | 0 | 4.75 |
| 14 | AP 14 | 386.72 | 3 | 0 | 4.49 |
| 15 | AP 15 | 385.72 | 3 | 1 | 3.94 |
| 16 | AP 16 | 423.8 | 1 | 0 | 6.84 |
| 17 | AP 17 | 400.74 | 3 | 0 | 4.87 |
| 18 | AP 18 | 379.35 | 1 | 0 | 6.76 |
| 19 | AP 19 | 388.36 | 3 | 0 | 5.08 |
| 20 | AP 20 | 374 | 2 | 0 | 5.98 |
| 21 | AP 21 | 409.04 | 3 | 0 | 5.81 |
| 22 | AP 22 | 409.04 | 3 | 0 | 5.81 |
| 23 | AP 23 | 444.22 | 1 | 0 | 7.14 |
| 24 | AP 24 | 452.85 | 2 | 0 | 6.57 |
| 25 | AP 25 | 425.77 | 2 | 1 | 6.25 |
| 26 | AP 26 | 466.83 | 3 | 1 | 6.19 |
| 27 | AP 28 | 466.83 | 3 | 1 | 6.19 |
| 28 | AP 29 | 491.92 | 1 | 0 | 8.33 |
| 29 | AP 34 | 463.82 | 2 | 1 | 7.44 |
| 30 | AP 35 | 450.79 | 3 | 0 | 6.26 |
| 31 | AP 36 | 455.81 | 4 | 1 | 5.07 |
| 32 | AP 37 | 476.84 | 2 | 1 | 2.96 |
| 33 | AP 38 | 497.86 | 3 | 0 | 6.95 |
| 34 | AP 39 | 453.79 | 3 | 1 | 6.04 |
| 35 | AP 40 | 451.81 | 2 | 0 | 6.23 |
| 36 | AP 42 | 454.77 | 4 | 0 | 4.42 |
| 37 | AP 43 | 486..77 | 6 | 0 | 5.3 |
| 38 | AP 47 | 495.87 | 3 | 0 | 7.48 |
| Abbreviations: Log P- partition coefficient; MW- molecular weight; nON-hydrogen bond acceptors; nOHNH- hydrogen bond donor. | |||||
Figure 2H-Bonding interaction of the ligand (analog 4) and Survivin protein
Figure 3Anti-apoptotic effect of Aplysin inhibit Survivin protein to induce apoptosis which acting at different points in Apoptotic Pathway
Binding energy of docked protein (Survivin) and novel Anticancer Analogs along with the standard Marine Compound Aplysin
| S.No. | Analogs | Binding Energy (kcal/mol) | Inhibition Constant uM | No. of Hydrogen Bond | Residue Interaction |
| 1 | Celecoxib | -6.65 | 13.43 | 5 | K62:HZ1 -: UNK0: N8 |
| K115:HZ3 -: UNK0: O5 | |||||
| K115:HZ3 -: UNK0: O6 | |||||
| UNK0: H39 - E63: OE2 | |||||
| UNK0: H40 - E63: OE2 | |||||
| 2 | Aplysin | -5.83 | 53.04 | 0 | No Hydrogen Bond |
| 3 | AP 1 | -6.31 | 23.75 | 0 | No Hydrogen Bond |
| 4 | AP 4 | -8.75 | 388.28 nM | 5 | K 62:HZ1 -: UNK0: BR17 |
| K62:HZ2 -: UNK0: O28 | |||||
| E 63:HN -: UNK0: O28 | |||||
| UNK0: N29 - E 65: OE1 | |||||
| UNK0: N29 - E 65:OE2 | |||||
| 5 | AP 10 | -7.12 | 6.01 | 2 | N111:HD22 -: UNK0:O18 |
| UNK0: N20 - A: G83:O | |||||
| 6 | AP 11 | -8.02 | 1.31 | 2 | K62:HZ2 -: UNK0:O28 |
| E63: HN -: UNK0:O28 | |||||
| 7 | AP 12 | -6.42 | 19.84 | 0 | No Hydrogen Bond Form |
| 8 | AP 13 | -6.03 | 37.98 | 0 | No Hydrogen Bond Form |
| 9 | AP 14 | -6.04 | 37.38 | 1 | K122:HZ3 -: UNK0:O20 |
| 10 | AP 15 | -5.49 | 94.94 | 0 | No Hydrogen Bond Form |
| 11 | AP 16 | -6.92 | 8.43 | 0 | No Hydrogen Bond Form |
| 12 | AP 18 | -6.76 | 11.07 | 0 | No Hydrogen Bond Form |
| 13 | AP 20 | -6.02 | 38.57 | 0 | No Hydrogen Bond Form |
| 14 | AP 21 | -5.22 | 148.2 | 0 | No Hydrogen Bond Form |
| 15 | AP 23 | -7.3 | 13.73 | 1 | S81: HG -: UNK0: BR17 |
| 16 | AP 24 | -6.76 | 11.08 | 1 | K122:HZ3 -: UNK0: CL15 |
| 17 | AP 26 | -6.97 | 7.83 | 0 | No Hydrogen Bond Form |
| 18 | AP 28 | -7.01 | 7.24 | 1 | K122:HZ3 -: UNK0:O9 |
| 19 | AP 29 | -8.72 | 407.25nM | 3 | K115:HZ3 -: UNK0:O30 |
| E63: HN -: UNK0:O29 | |||||
| K62:HZ2 -: UNK0:O29 | |||||
| 20 | AP 36 | -7.6 | 2.67 | 1 | K115:HZ3 -: UNK0:O25 |
| 21 | AP 37 | -7.01 | 7.25 | 4 | S81: HG -: UNK0:O29 |
| K122:HZ3 -: UNK0:O9 | |||||
| UNK0:O29 - S81:OG | |||||
| UNK0:O29 - S81:O | |||||
| 22 | AP 40 | -6.97 | 7.76 | 2 | A85: HN -: UNK0:O25 |
| N111:HD22 -: UNK0:O25 | |||||
| 23 | AP 43 | -8.72 | 406.37nM | 5 | K62:HZ2 -: UNK0:O27 |
| E63: HN -: UNK0:O27 | |||||
| K115:HZ3 -: UNK0:O28 | |||||
| N119:HD22 -: UNK0:O25 | |||||
| K122:HZ3 -: UNK0:O26 | |||||
| 24 | AP 47 | -5.88 | 48.72 | 2 | R108:HH11 -: UNK0:O24 |
| R108:HH11 -: UNK0:O25 |