Molecular Docking of Vascular Endothelial Growth ...

International Journal of Research in Pharmaceutical and Biomedical Sciences

ISSN: 2229-3701

_________________________________________Research Article

Molecular Docking of Vascular Endothelial Growth Factor with Phytochemicals for Anti-Angiogenesis Rachana R. Desai1, Drushti H. Bhatt1, Yogesh T. Jasrai1*, Himanshu A. Pandya1 and Rakesh M. Rawal2 1Department

of Bioinformatics, Applied Botany Centre, University School of Sciences,

Gujarat University, Ahmedabad, Gujarat, India. 2Division

of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology,

The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India. _________________________________________________________________________________ ABSTRACT The vascular endothelial growth factor (VEGF) pathway is well recognized as one of the key regulators of angiogenesis. The deregulated angiogenesis leading to neovascularization is an indispensible phenomenon in solid tumour growth and metastasis. An anti-VEGF monoclonal antibody (Bevacizumab) has been used as a drug agent for anti-angiogenesis in combination with chemotherapy. The most significant adverse event observed with Bevacizumab includes fetal bleeding and proteinuria in 38% patients. To avoid such side effects, the natural compounds (phytochemicals) as ligand against VEGF in comparison with Bevacizumab using molecular docking studies and post processing of docking results were studied, where Homorragintonine as a top scoring natural(phytochemical)was obtained. Generating scientific hypothesis towards regulation of angiogenesis and its role in tumor growth and metastasis is of prime importance. This will provide newer avenues in the future to develop specific anti-angiogenic agents from natural sources that may offer a potential therapy for cancer and angiogenic diseases. INTRODUCTION Angiogenesis and Vascular Endothelial Growth Factor (VEGF) Angiogenesis is a difficult process, where angiogenic endothelial cells undergo a complex sequence of events that includes the secretion of metallo-proteases and other matrix-degrading enzymes, cell migration into the newly created space, endothelial cell division and proliferation, including new blood vessel formation2,21. The role of vascular endothelial growth factor (VEGF) in the regulation of angiogenesis has been studied where VEGF family comprising seven secreted glycoproteins that are designated VEGF-A, VEGFB, VEGF-C, VEGF-D, VEGF-E, placental growth factor (PlGF) and VEGF-F are involved3,9,10,22. The VEGF exert their biological effect through interaction with their receptors, the trans-membrane tyrosine kinase which upon binding with their ligands to the extracellular domain of the receptor,activate a cascade of downstream proteins after the dimerization and auto-phosphorylation of the intracellular receptor tyrosine kinases 4,5,10,20.

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Role of VEGF as a Target for Tumor Angiogenesis The endothelial cells are thought to be an ideal target for therapies directed against cancer cells because of genomic stability25,26. VEGF is secreted from the over expressive tumor and binds to high affinity signalling receptors on the endothelial cells of existing blood vessels, which leads to the formation of new blood capillaries, which provide the necessary nutrients for tumor cell survival and tumor growth1. So, Anti-VEGF agents and other VEGF inhibitors has been approved as a first-line treatment for treatment of angiogenesis in combination with chemotherapy11,12,13,17,23. There are some small molecules inhibiting VEGF receptors or Endothelial growth factor receptor. They inhibit inhibiting the activity of specific receptor tyrosine kinases [vatalanib (PTK787/ZK) or erlotinib (OSI-774) and gefitinib (ZD1839), respectively] that are integral to the VEGF and EGFR signalling cascades10,13. The humanized anti-VEGF monoclonal antibody, Bevacizumab has been prescribed for treatment of malignant cells7,11. The results from a large, randomized Phase III clinical trial for patients with previously untreated advanced non-squamous, nonsmall cell lung cancer show that those patients who

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received Bevacizumab in combination with standard chemotherapy (paclitaxel and carboplatin) lived longer than patients who received the same chemotherapy without Bevacizumab7,11,15,19. The Bevacizumab not only used as anti-angiogenesis but also used in treatment of breast cancer, colorectal cancer, prostate cancer etc6,7,8. The lifethreatening adverse effect of Bevacizumab therapy was proteinuria. The hypertension and bleeding disorder were also observed due to this therapy25. Thus, natural compounds present in foods and their derivatives have practical advantages with regard to availability, suitability for oral application, regulatory approval and mechanisms of action. Although there is an increasing focus on designer therapeutic agents, the broad spectrum of activity of natural products across multiple signalling pathways remains inadequately explored. Briefly evidence of dietary agents obtained from fruits and vegetables which can act to modulate the effect on VEGF were presented along with their contribution for the prevention of angiogenesis. Docking studies and Drug-Likeliness Molegro Virtual Docker is an invaluable tool in modern drug discovery which offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. The MVD has been shown to yield higher docking accuracy than other state-of-the-art docking products (MVD: 87%, Glide: 82%, Surflex: 75%, FlexX: 58%)29. The OSIRIS Property Explorer is an integral part of Actelion's ( in-house substance registration system. Prediction results are valued and colour coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption were shown in red. Whereas a green color indicates drug-conform behaviour. It covers the properties like toxicity risk assessment, clogP prediction, solubility prediction, molecular weights, fragment based drug-likeness prediction, overall drug-Likeness Score28. COMPUTATIONAL METHOD Several offline tools, online tools and databases were used to accomplish this work. The process was started by retrieving crystal structure of VEGF (PDB ID: 1FLT) from Protein Data Bank30. Next,

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the one hundred and six natural compounds were derived from PubChem .This database contains substance database, compound database and BioAssay database. The library of ligands was obtained from Compound Pubchem. The detailed information like molecular weight, 2D and 3D structures, IUPAC name and H-donor/acceptor of compounds can be obtained from PubChem31. Further, the interacting residues within the pocket of receptor had been identified by PDBSum. So, the probable binding site,which has been made between ligand and protein, number of residues of protein and type of proteins for docking the molecules can be known32. Finally, Docking studies and drug-Likeliness of natural compounds and Bevacizumab (PubChem ID: 24801581), with combination of VEGF (PDB ID: 1FLT) was observed using MVD and OSIRIS respectively29,28. RESULTS AND DISCUSSION To obtain the desire output against available drug for tumor angiogenesis, the ligands (phytochmicals) were taken and docked with VEFG [Figure 1] along with Bevacizumab in MVD by which all the ligands were embedded within cavity, were observed forming hydrogen bonds with same position as Bevacizumab established (Lys 107 and Glu 67) [Figure 1]. 7 out of 106 natural ligands were found, to require lower energy as compared to Bevacizumab, which is used as therapeutic agent for Anti-angiogenesis treatment[Table 1]. Bevacizumab requires -115.54 Kcal/Mol where as Homoharringtonine (Cephalotaxus harringtonia tree), Limonin (Citric fruits) and Licoagrochalcone (root constituent of Glycyrrhiza glabra) require -153.871 Kcal/mol,146.003 Kcal/mol and -142.803 Kcal/mol respectively. These results gave alternative approach for anti-angiogenesis treatment by natural compounds which can be obtained from regular dietary products. The Gossypol (Cotton plant), Ginkgetin (Ginkgo biloba leaves) and Psoralidin (seeds of Psoralea corylifolia) require less energy such as -141.993 Kcal/mol, -140.004 Kcal/mol and -139.252 Kcal/mol respectively [Table 1].


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A

B

ISSN: 2229-3701

C

C

D

D

Fig. 1: A. 3D structure of VEGF (PDB:ID:1FLT) taken for PDBSum, B. Surface view of VEGF with Bevacizumab within cavity, C. Secondary structure of VEGF with library of Natural compounds, D. Figure represents the Position of hydrogen bond (Lys 107 and Glu 67) between natural ligandsD (thin C stick view) and VEGF (ball and stick Green view). B Table 1: Docking results of reported inhibitor and natural ligands PubChem ID

Ligand Name

24801581 285033 179651 11099375 3503 66065 5271805 5281806

Bevacizumab Homoharringtonine Limonin Licoagrochalcone Gossypol Bergenin Ginkgetin Psoralidin

MolDock Score Kcal/mol -115.54 -153.871 -146.003 -142.803 -141.993 -141.716 -140.004 -139.252

Along with the docking result, drug-likeliness properties for top seven compounds with OSIRIS tool was checked and observed that some of natural compounds gave good score as compared to Bevacizumab. Homoharringtonine, licoagrochalcone A, Bergenine have molecular weight 303, 324 and 328 respectively where as Bevacizumab has molecular weight 390.Similarly, Homoharringtinine and Licoagrochalcone having -

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Rerank Score

HBond

-90.7975 -94.2987 -11.0039 -101.032 -100.376 -88.4438 -102.588 -113.542

-6.15863 -15.3552 -15.4304 -11.2062 -5.27052 -4.53926 -5.0000 -3.07095

3.43 and -3.89 solubility, which are lesser than the observation for Bevacizumab. But Bergenin and Homoharringtonine have lower cLogP value -1.02 and 1.8 respectively, means they have lowest hydrophobicitis and highest absorption or permeation capabilities. The Drug-Scores of all compounds are within 0.08 to 0.85 range [Table 2]. Further colour representation of Toxicity Risk which includes mutagenic, tumoregenic, irritant,


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reproductive effective parameters demonstrated mutagenic property along with gossypol having green colour which represents the drug conformer irritant property. property. On the other hand, ginkgetin showed Table 2: Results OSIRIS tool with reported inhibitor and natural ligands Natural Ligand

cLopP

Bavicizumab

2.5

Homoharringtonine licoagrochalcone A Bergenin Psoralidin gossypol Ginkgetin

1.8 4.33 -1.02 3.2 3.84 5.29

Solubility Molecular Weight Reported Inhibitor -2.67 390 Natural Ligands -3.43 303 -3.89 324 -1.21 328 -3.64 354 -4.99 506 -6.5 552

CONCLUSION The protein-ligand interaction plays a significant role in structure-based drug designing. It is clearly demonstrated that the docking approach utilized in the study is successful in finding novel ligands with anti-angiogenesis activity. The study revealed Homoharringtonine, Licoagrochalcone as potential drug lead compounds showing better binding efficiency with VEGF as targets. Further QSAR studies focusing on semisynthetic derivatization of these phytochemicals will be useful in assessing their role in in vitro angiogenesis reversal capability. REFERENCES 1. Terman B. I. and Stoletov K. V.; VEGF and Tumor Angiogenesis , Departments of Medicine and Pathology ,Albert Einstein College of Medicine Einstein Quart. J. Biol. and Med.; 2001; 18:59-66 2. Bruick R. K. and McKnight S. L.; Building better vasculature; Genes Division; 2001; 15: 2497-2502. 3. Ball S. G., Shuttleworth C. A., and Kielty C. M.; Vascular endothelial growth factor can signal through platelet-derived growth factor receptors; The Journal of Cell Biology; 2007; 177[3]:489-500. 4. Abali H. and Gullu I. H.; Old antihypertensives as novel antineoplastics: angiotensin-I-converting enzyme inhibitors and angiotensin II type 1 receptor antagonists; Medical Hypotheses; 2002; 59(3): 344-348. 5. Duda D. G., Batchelor T. T., Willet C. G. and Jain R. K.; VEGF-targeted cancer therapy strategies: current progress, hurdles and future prospects; Elsevier Ltd; 2004; 13(6):223-230. 6. Boige V. and Malka D.; Therapeutic strategies using VEGF inhibitors in colorectal cancer; Bull Cancer; 2005; 92:29-36. 7. Bossung V. and Harbeck N.; Angiogenesis inhibitors in the management of breast

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8.

9.

10.

11.

12.

13.

14.

15.

Drug-Likeliness

Drug-Score

4.15

0.82

3.95 0.73 -1.45 -1.91 -3.42 2.52

0.850 0.58 0.55 0.44 0.15 0.08

cancer; Current Opin Obstet Gynecol; 2010; 22(1): 79-86. Kluetz P. G., Figg W. D., Pharm D., and Dahut W. L.; Angiogenesis Inhibitors in the treatment of Prostate Cancer; Expert Opin Pharmacotherapy ; 2010; 11(2): 233–247 Lee K., Jeong K., Lee Y., Ji Yeon Song, Kim M. S., Lee G. S. and Kim Y.; Pharmacophore modeling and virtual screening studies for new VEGFR-2 kinase inhibitors; European Journal of Medicinal Chemistry; 2010; 45:54205427. Otrock Z. K., Makarem J. A. and Shamseddine A. I.; Vascular endothelial growth factor family of ligands and receptors: Review; Blood Cells, Molecules, and Diseases; 2007; 38:258– 268. Napoleone Ferrara a, Hillan K. J. and William N.; Bevacizumab (Avastin), a humanized anti-VEGF monoclonal antibody for cancer therapy; Biochemical and Biophysical Research Communications; 2005; 332(2):328–35. Bender G. J. and Yamashiro D. J.; Clinical development of VEGF signaling pathway inhibitors in childhood solid tumors.; Oncologist; 2011; 16(11): 1614-1625 Morabito A. and Maio E. D.; Tyrosine kinase inhibitors of vascular endothelial growth factor receptors in clinical trials: current status and future directions; Oncologist; 2006; 11(7): 753-764. Brower, V. ; Evidence of efficacy: researchers investigating markers for angiogenesis inhibitors.; Natl Cancer Institute; 2003; 95(19): 1425-1427. Tabernero J.; The Role of VEGF and EGFR Inhibition: Implications for Combining Anti -VEGF and Anti-EGFR Agents; Molecular Cancer Research; 2007;5:203-220.


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16. Cardones, A. R. and Banez L. L.; VEGF inhibitors in cancer therapy; Current Pharmaceutics; 2006; 12(3): 387-394. 17. Carter, S. K.; Clinical strategy for the development of angiogenesis inhibitors; Oncologist; 2000; 5 51-54. 18. Cascinu, S.,and Graziano F.; Differences of vascular endothelial growth factor (VEGF) expression between liver and abdominal metastases from colon cancer. Implications for the treatment with VEGF inhibitors; Clinical Expert Metastasis; 2000; 18(8): 651-655. 19. Langer, C. J. and Natale R. B.; The emerging role of vascular endothelial growth factor receptor tyrosine kinase inhibitors; Semin Oncology; 2005; 32:2329. 20. Choueiri, T. K.; VEGF inhibitors in metastatic renal cell carcinoma: current therapies and future perspective; Current Clinical Pharmacology; 2011; 6(3): 164168. 21. Cébe-Suarez S., Zehnder-Fjällman A. and Ballmer-Hofer K.;The role of VEGF receptors in angiogenesis; complex partnerships; Cellular and Molecular Life Sciences; 2006; 63:601–615. 22. Fayette, J. and Soria J. C.; Use of angiogenesis inhibitors in tumour treatment.; European Journal of Cancer; 2005; 41(8): 1109-1116. 23. Kazazi-hyseni F., Beijnen J. H. and Schellensa H. M.; Bevacizumab; The Oncologist; 2010;15:819–825 24. Xuri Li, Kumar A., Zhang F., Lee C. and Tang Z.; Complicated life, complicated VEGF-B; Molecular Medicine; 2012, 18(2):119-27.

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25. Frumovitz M. and Sood A.K.; Vascular Endothelial Growth Factor (VEGF) Pathway as a Therapeutic Target in Gynaecologic Malignancies; Gynecol Oncology.; 2007; 104(3): 768–778. 26. Sood A. K., Coleman R. L. and EllisMoving L. M.; Beyond Anti– Vascular Endothelial Growth Factor Therapy in Ovarian Cancer; American Society of Clinical Oncology; 2011; 30(4):345-7. 27. Wu1 H.C. and Li P.C.; Proteins Expressed on Tumor Endothelial Cells as Potential Targets for Anti-Angiogenic Therapy; Journal of Cancer Molecules; 2008; 4(1): 17-22. 28. OSIRIS Property Explorer, Thomas Sander, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, 4123 Allschwil, Switzerland, http://www.organic-

chemistry.org/prog/peo/ 29. Thomsen R. and Christensen M. H.; MolDock: A New Technique for HighAccuracy Molecular Docking; Journal of Medicinal Chemistry; 2006;49(11);3315 3321. 30. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.E., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T. and Tasumi M.; The Protein Data Bank: A Computer-based Archival File For Macromolecular Structures; Journal of. Molecular. Biology; 112 (1977): 535. 31. http://pubchem.ncbi.nlm.nih.gov/help.html 32. Laskowski R. A., Chistyakov V. V. and Thornton J. M.; PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids; Nucleic Acids Research; 2005; 33: 266– 268.


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