Screening of novel alkaloid inhibitors for vascular endothelial growth factor in cancer cells: an integrated computational approach |
Shahik, Shah Md.
(Molecular Biology Department, AFC Agro Biotech Ltd.)
Salauddin, Asma (Bioinformatics Division, Disease Biology and Molecular Epidemiology Research Group(dBme)) Hossain, Md. Shakhawat (Bioinformatics Division, Disease Biology and Molecular Epidemiology Research Group(dBme)) Noyon, Sajjad Hossain (Bioinformatics Division, Disease Biology and Molecular Epidemiology Research Group(dBme)) Moin, Abu Tayab (Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong) Mizan, Shagufta (Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong) Raza, Md. Thosif (Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong) |
1 | Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 2006;34:W116-W118. DOI |
2 | Avgerinos KI, Spyrou N, Mantzoros CS, Dalamaga M. Obesity and cancer risk: emerging biological mechanisms and perspectives. Metabolism 2019;92:121-135. DOI |
3 | Fouad YA, Aanei C. Revisiting the hallmarks of cancer. Am J Cancer Res 2017;7:1016-1036. |
4 | Ramjiawan RR, Griffioen AW, Duda DG. Anti-angiogenesis for cancer revisited: is there a role for combinations with immunotherapy? Angiogenesis 2017;20:185-204. DOI |
5 | Parangi S, O'Reilly M, Christofori G, Holmgren L, Grosfeld J, Folkman J, et al. Antiangiogenic therapy of transgenic mice impairs de novo tumor growth. Proc Natl Acad Sci U S A 1996;93: 2002-2007. DOI |
6 | Cross MJ, Claesson-Welsh L. FGF and VEGF function in angiogenesis: signalling pathways, biological responses and therapeutic inhibition. Trends Pharmacol Sci 2001;22:201-207. DOI |
7 | Wise LM, Stuart GS, Jones NC, Fleming SB, Mercer AA. Orf virus IL-10 and VEGF-E act synergistically to enhance healing of cutaneous wounds in mice. J Clin Med 2020;9:1085. DOI |
8 | Alvarez-Aznar A, Muhl L, Gaengel K. VEGF receptor tyrosine kinases: key regulators of vascular function. Curr Top Dev Biol 2017;123:433-482. DOI |
9 | Elice F, Rodeghiero F. Side effects of anti-angiogenic drugs. Thromb Res 2012;129 Suppl 1:S50-53. DOI |
10 | Priya R, Sumitha R, Doss CG, Rajasekaran C, Babu S, Seenivasan R, et al. Molecular docking and molecular dynamics to identify a novel human immunodeficiency virus inhibitor from alkaloids of Toddalia asiatica. Pharmacogn Mag 2015;11(Suppl 3):S414-S422. |
11 | Holmes DI, Zachary I. The vascular endothelial growth factor (VEGF) family: angiogenic factors in health and disease. Genome Biol 2005;6:209. DOI |
12 | Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res 2014;42:D485-D489. DOI |
13 | Sterling T, Irwin JJ. ZINC 15: ligand discovery for everyone. J Chem Inf Model 2015;55:2324-2337. DOI |
14 | Gao YD, Huang JF. An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level. Dongwuxue Yanjiu 2011;32:262-266. |
15 | Lagorce D, Maupetit J, Baell J, Sperandio O, Tuffery P, Miteva MA, et al. The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. Bioinformatics 2011; 27:2018-2020. DOI |
16 | Shojaei F. Anti-angiogenesis therapy in cancer: current challenges and future perspectives. Cancer Lett 2012;320:130-137. DOI |
17 | Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer 2015;136:E359-E386. DOI |
18 | Liu K, Kokubo H. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations: a cross-docking study. J Chem Inf Model 2017;57:2514-2522. DOI |
19 | Zachary I. Signaling mechanisms mediating vascular protective actions of vascular endothelial growth factor. Am J Physiol Cell Physiol 2001;280:C1375-1386. DOI |
20 | Surman M, Janik ME. Stress and its molecular consequences in cancer progression. Postepy Hig Med Dosw (Online) 2017;71: 485-499. |
21 | DeSantis CE, Miller KD, Dale W, Mohile SG, Cohen HJ, Leach CR, et al. Cancer statistics for adults aged 85 years and older, 2019. CA Cancer J Clin 2019;69:452-467. DOI |
22 | Yehya AH, Asif M, Petersen SH, Subramaniam AV, Kono K, Majid A, et al. Angiogenesis: managing the culprits behind tumorigenesis and metastasis. Medicina (Kaunas) 2018;54:8. DOI |
23 | Nishida N, Yano H, Nishida T, Kamura T, Kojiro M. Angiogenesis in cancer. Vasc Health Risk Manag 2006;2:213-219. DOI |
24 | Dameron KM, Volpert OV, Tainsky MA, Bouck N. Control of angiogenesis in fibroblasts by p53 regulation of thrombospondin-1. Science 1994;265:1582-1584. DOI |
25 | Neufeld G, Cohen T, Gengrinovitch S, Poltorak Z. Vascular endothelial growth factor (VEGF) and its receptors. FASEB J 1999; 13:9-22. DOI |
26 | Niu G, Chen X. Vascular endothelial growth factor as an anti-angiogenic target for cancer therapy. Curr Drug Targets 2010;11: 1000-1017. DOI |
27 | Holmgren L, O'Reilly MS, Folkman J. Dormancy of micrometastases: balanced proliferation and apoptosis in the presence of angiogenesis suppression. Nat Med 1995;1:149-153. DOI |
28 | Roskoski R Jr. Vascular endothelial growth factor (VEGF) signaling in tumor progression. Crit Rev Oncol Hematol 2007;62:179-213. DOI |
29 | Matsumoto T, Claesson-Welsh L. VEGF receptor signal transduction. Sci STKE 2001;2001:re21. |
30 | Melincovici CS, Bosca AB, Susman S, Marginean M, Mihu C, Istrate M, et al. Vascular endothelial growth factor (VEGF): key factor in normal and pathological angiogenesis. Rom J Morphol Embryol 2018;59:455-467. |
31 | Claesson-Welsh L. VEGF receptor signal transduction: a brief update. Vascul Pharmacol 2016;86:14-17. DOI |
32 | Peach CJ, Mignone VW, Arruda MA, Alcobia DC, Hill SJ, Kilpatrick LE, et al. Molecular pharmacology of VEGF-A isoforms: binding and signalling at VEGFR2. Int J Mol Sci 2018;19:1264. DOI |
33 | Carden CP, Larkin JM, Rosenthal MA. What is the risk of intracranial bleeding during anti-VEGF therapy? Neuro Oncol 2008; 10:624-630. DOI |
34 | Kilickap S, Abali H, Celik I. Bevacizumab, bleeding, thrombosis, and warfarin. J Clin Oncol 2003;21:3542. DOI |
35 | Wu JB, Tang YL, Liang XH. Targeting VEGF pathway to normalize the vasculature: an emerging insight in cancer therapy. Onco Targets Ther 2018;11:6901-6909. DOI |
36 | Risau W. Mechanisms of angiogenesis. Nature 1997;386:671-674. DOI |
37 | Elice F, Rodeghiero F. Bleeding complications of antiangiogenic therapy: pathogenetic mechanisms and clinical impact. Thromb Res 2010;125 Suppl 2:S55-57. DOI |
38 | Tian W, Chen C, Lei X, Zhao J, Liang J. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 2018; 46:W363-W367. DOI |
39 | Chakraborty C, Mallick B, Sharma AR, Sharma G, Jagga S, Doss CG, et al. Micro-environmental signature of the interactions between druggable target protein, dipeptidyl peptidase-IV, and anti-diabetic drugs. Cell J 2017;19:65-83. |
40 | Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res 2019;47:D1102-D1109. DOI |
41 | O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: an open chemical toolbox. J Cheminform 2011;3:33. DOI |
42 | Stirland DL, Nichols JW, Miura S, Bae YH. Mind the gap: a survey of how cancer drug carriers are susceptible to the gap between research and practice. J Control Release 2013;172:1045-1064. DOI |
43 | Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455-461. DOI |
44 | Alqahtani S. In silico ADME-Tox modeling: progress and prospects. Expert Opin Drug Metab Toxicol 2017;13:1147-1158. DOI |
45 | Sander T, Freyss J, Korff M, Reich JR, Rufener C. OSIRIS, an entirely in-house developed drug discovery informatics system. J Chem Inf Model 2009;49:232-246. DOI |
46 | Miguel JS, Weisel K, Moreau P, Lacy M, Song K, Delforge M, et al. Pomalidomide plus low-dose dexamethasone versus high-dose dexamethasone alone for patients with relapsed and refractory multiple myeloma (MM-003): a randomised, open-label, phase 3 trial. Lancet Oncol 2013;14:1055-1066. DOI |
47 | Hirai M, Nakagawara A, Oosaki T, Hayashi Y, Hirono M, Yoshihara T. Expression of vascular endothelial growth factors (VEGF-A/VEGF-1 and VEGF-C/VEGF-2) in postmenopausal uterine endometrial carcinoma. Gynecol Oncol 2001;80:181-188. DOI |
48 | Hisano Y, Hla T. Bioactive lysolipids in cancer and angiogenesis. Pharmacol Ther 2019;193:91-98. DOI |
49 | Sitohy B, Nagy JA, Dvorak HF. Anti-VEGF/VEGFR therapy for cancer: reassessing the target. Cancer Res 2012;72:1909-1914. DOI |
50 | Ruvinsky I, Silver LM, Gibson-Brown JJ. Phylogenetic analysis of T-Box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. Genetics 2000; 156:1249-1257. DOI |
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