Mydhili Govindarasu, Mariyappan Palani, Manju Vaiyapuri


Objective: The objective of this research was to formulate the binding energies and interaction of amino acid residues in kaempferitrin with different types of apoptotic and inflammatory proteins of colon cancer.

Methods: AutoDock Vina and MGL tool were used for docking calculations. Both programs require the pdbqt input files and allow for flexibility of all the torsional bonds of small molecules. Discovery Studio Visualizer v3.5 was used for removal of water molecules and ligands and the pymol program was used to do analysis of the docking with various apoptotic proteins BAX, Bcl-2, COX-2, Protein kinase B.

Results: In our study was developed binding energy scoring function of kaempferitrin docked with different types of inflammatory proteins and apoptotic proteins. Binding score values for-6.9 (BAX),-7.2 (Bcl-2),-7.3 (caspase-3),-8.8 (Cox-2),-7.4 (Cytochrome P450),-6.7 (Proteinase kinase B),-8.0 (TNF-α) and-7.2 (VEGF) kcal/mol, respectively. Amino acid interaction of kaempferitrin with proteins for ARG-25, LEU-52, ASN-54, PHE-55, GLU-17, LYS-14, TRP-22, THR-21 GLY-16 (Protein Kinase B), ASP-102, ASN-48, GLN-52, ASP-104 (BAX), GLU-176, TRP-173, GLU-132, PHE-135 (Bcl-2), SER-249, ASP-2, ASN-208, GLN-217, LEU-242 (Caspase 3), TYR-55, HIS-39, SER-49, GLU-322, GLY-326 (COX-2), SER-95, LEU-94, ARG-82, VAL-123, ALA-96 (TNF-α), ASP-414, LYS-322, GLU-326, GLU-416, GLU-438, ALA-439, GLU-437 (Cytochrome P450) and LEU-47, GLN-46, CYS-61, CYS-60, ASP-63, GLU-67, GLY-65, LEU-66 (VEGF) respectively.

Conclusion: The results obtained in this research work clearly indicated the docking scores of apoptotic and Inflammatory proteins imply that kaempferitrin is an effective inhibitory compound for colon cancer.


Kaempferitrin, AutoDock Vina, MGL Tool, Protein Kinase B, Bcl-2

| PDF | HTML |


Karthi N, Kalaiyarasu T, Kandakumar S, Mariyappan P, Manju V. Pelargonidin induces apoptosis and cell cycle arrest via a mitochondria mediated intrinsic apoptotic pathway in HT29 cells. RSC Adv 2016;6:45064-76.

Ragunath M, Nadanasabapathy S, Manju V. Anti-inflammatory and proapoptotic effects of umbelliferone in colon carcinogenesis. Hum Exp Toxicol 2016;35:1-14.

Valentina P, Assunta S, Emma M, Roberta B, Raffaella S, Giulia R, Annapina R. 5-FU targets rpL3 to induce mitochondrial apoptosis via cystathionine-β-synthase in colon cancer cells lacking p53. Oncotarget 2016;7:50333-48.

Lin J, Page C, Jin X, Sethi AO, Patel R, Nunez G. Suppression activity of pro-apoptotic gene products in cancer cells, a potential application for cancer gene therapy. Anticancer Res 2001;21:831-9.

Kaleigh F, Manabu K. Evading apoptosis in cancer. Trends Cell Biol 2013;23:620-33.

Alonso-Castro AJ, Ortiz-Sanchez E, Garcia-Regalado A, Ruiz G, Nunez-Martinez JM, Gonzalez-Sanchez I, et al. Kaempferitrin induces apoptosis via intrinsic pathway in HeLa cells and exerts antitumor effects. J Ethnopharmacol 2013;145:476-89.

Rong T. Chemistry and biochemistry of dietary polyphenols. Nutrients 2010;2:1231-46.

Kalaiyarasu T, Karthi N, Sharmila Gowri V, Manju V. In vitro assessment of antioxidant and antibacterial activity of green synthesized silver nanoparticles from digitaria radicosa leaves. Asian J Pharm Clin Res 2016;9:297-302.

The Human Metabolome Database. Available from: http:// [Last accessed on 01 May 2017].

Soussi T, Lozano G. p53 mutation heterogeneity in cancer. Biochem Biophys Res Commun 2005;331:834-42.

Fredericks E, Dealtry G, Roux S. Molecular aspects of colorectal carcinogenesis: a review. J Cancer Biol Res 2015;3:1057.

Mariyappan P, Karthi N, Manju V. Computational studies on different types of apoptotic proteins docked with a dietary flavonoid eriodictyol in colon cancer. Asian J Pharm Clin Res 2017;10:223-6.

Ranjan S, Dasgupta N, Chinnappan S, Ramalingam C, Kumar A. A novel approach to evaluate titanium dioxidenanoparticle–protein interaction through docking: an insight into mechanism of action. Proc Natl Acad Sci India B Biol Sci; 2015. p. 1-7.

Staal SP, Hartley JW, Rowe WP. Isolation of transforming murine leukemia viruses from mice with a high incidence of spontaneous lymphoma. Proc Natl Acad Sci USA 1977;74:3065-7.

Staal SP. Molecular cloning of the akt oncogene and its human homologues AKT1 and AKT2: amplification of AKT1 in a primary human gastric adenocarcinoma. Proc Natl Acad Sci USA 1987;84:5034-7.

Vivanco I, Sawyers CL. The phosphatidylinositol 3-kinase-AKT pathway in human cancer. Nat Rev Cancer 2002;2:489-501.

Alicia H, Israel V, Rafael C, Fabian L, Ping J, Yongping Y, et al. Docking of protein kinase B inhibitors: implications in the structure-based optimization of a novel scaffold. Chem Biol Drug Des 2010;76:269-76.

Sefika KU, Seval A, Elif O. Virtual screening and docking of potential protein kinase b inhibitors. Cell 2012;102:60-1.

Debatin KM. Apoptosis pathways in cancer and cancer therapy. Cancer Immunol Immun 2004;53:153-9.

Suzuki M, Youle RJ, Tjandra N. Structure of bax: coregulation of dimer formation and intracellular localization. Cell 2000; 103:645-54.

Reed JC. Mechanisms of apoptosis. Am J Pathol 2000;157:1415-30.

Wong RSY. Apoptosis in cancer: from pathogenesis to treatment. J Exp Clin Cancer Res 2011;30:87.

Gao D, Xu Z, Qiao P, Liu S, Zhang L, He P, et al. Cadmium induces liver cell apoptosis through caspase-3A activation in purse red common carp (Cyprinus carpio). Plos One 2013;8:83423.

Gupta RA, Dubois RN. Colorectal cancer prevention and treatment by inhibition of cyclooxygenase-2. Nat Rev Cancer 2001;1:11–21.

Han JA. Cyclooxygenase-2 promotes cell proliferation, migration and invasion in U2OS human osteosarcoma cells. Exp Mol Med 2007;39:469-76.

AI-Fayez M, Cai H, Tunstall R, Steward WP, Gescher AJ. Differential modulation of cyclooxygenase-mediated prostaglandin production by the putative cancer chemo-preventive flavonoids tricin, apigenin and quercetin. Cancer Chemother Pharmacol 2006;58:816-25.

O'Leary KA, de Pascual-Tereasa S, Needs PW, Bao YP, O’Brien NM, Williamson G. Effect of flavonoids and vitamin E on cyclooxygenase-2 (COX-2) transcription. Mutat Res 2004;551: 245-54.

Isnatin M, Jumina J, Sofia MH, Mustofa M. In silico molecular docking of xanthone derivatives as cyclooxygenase-2 inhibitor agents. Int J Pharm Pharm Sci 2017;9:98-104.

Sara C, Salvatore A, Angela Di C, Giovanna P, Adele P, Manuela S, et al. Synthesis, biological evaluation and docking analysis of a new series of methylsulfonyl and sulfamoyl acetamides and ethyl acetates as potent COX-2 inhibitors. Bioorg Med Chem 2015;23:810-20.

Esposito E, Cuzzocrea S. TNF-alpha as a therapeutic target in inflammatory diseases, ischemia reperfusion injury and trauma. Curr Med Chem 2009;1:3152-67.

Nelson DR. Cytochrome P450 nomenclature. Methods Mol Biol 2004;320:1-10.

Guengerich FP. Cytochrome P450 and chemical toxicology. Chem Res Toxicol 2008;21:70-83.

Zanger U. The CYP2D Subfamily. In: C Ioannides. Ed. Cytochromes P450: Role in the metabolism and toxicity of drugs and other xenobiotics. Royal Society of Chemistry; 2008. p. 241-75.

Xuelin Z, Yan W, Tao H, Penelope MY, John W, Yiu Wa K, et al. Enzyme kinetic and molecular docking studies for the inhibitions of miltirone on major human cytochrome P450 isozymes. Phytomedicine 2013;20:367-74.

Bao P, Kodra A, Tomic-Canic M, Golinko MS, Ehrlich HP, Brem H. The role of vascular endothelial growth factor in wound healing. J Surg Res 2009;153:347-58.

Nissen NN, Polverini PJ, Koch AE, Volin MV, Gamelli RL, DiPietro LA. Vascular endothelial growth factor mediates angiogenic activity during the proliferative phase of wound healing. Am J Pathol 1998;152:1445-52.

Gaudry M, Bregerie O, Andrieu V, Benna J, Pocidalo MA, Hakim J. Intracellular pool of vascular endothelial growth factor in human neutrophils. Blood 1997;90:4153-61.

Berse B, Brown LF, Van de Water L, Dvorak HF, Senger DR. Vascular permeability factor (vascular endothelial growth factor) gene is expressed differentially in normal tissues, macrophages, and tumors. Mol Biol Cell 1992;3:211-20.

Shamsuddin SK, Amin Malik Shah AM, Muhammad AI, Aman Shah AM, Majed M, Rosenani SM. Designing the angiogenic inhibitor for brain tumor via disruption of VEGF and IL17A expression. Eur J Pharm Sci 2016;93:304-18.

Feinstein WP, Brylinski M. Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 2015;7:18.

Alhossary A, Handoko SD, Mu Y, Kwoh CK. Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinfo 2015;31:214-6.

About this article




Kaempferitrin, AutoDock Vina, MGL Tool, Protein Kinase B, Bcl-2





Additional Links

Manuscript Submission


International Journal of Pharmacy and Pharmaceutical Sciences
Vol 9, Issue 9, 2017 Page: 199-204

Online ISSN



14 Views | 0 Downloads

Authors & Affiliations

Mydhili Govindarasu
Molecular Oncology Lab, Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India

Mariyappan Palani
Molecular Oncology Lab, Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India

Manju Vaiyapuri
Molecular Oncology Lab, Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India

Article Tools


  • There are currently no refbacks.