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Krithika Vasanth Naik, Nilofar Khan,
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- Research Intern, Research Intern BioNome for Genomics and Bioinformatics Solution,, BioNome for Genomics and Bioinformatics Solution, Bengaluru, Bengaluru India, India
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Abstract
nCyclin Dependent Kinase 2 (CDK 2) is a protein synthesized by Calotropis procera. It is known to be responsible for causing cancer in a human body. Studies have presented significance of the phytochemicals to inhibit the CDK 2 protein. Adsorption, distribution, metabolism and excretion (Swiss ADME) and Pubchem were the pharmacological tools which were used to check Molecular weight, which should be less than 500D, acceptors less than 10 and donors less than 5, Log P less than 5 and Gastrointestinal (GI) absorption should be high and Blood Bank Barrier (BBB) is also identified. If the druglikeness is absent and has 2 violations then there will be no drug discovery. Using Pubchem the ligands were searched and the Simplified molecular-input line-entry system (SMILES) was copied and pasted to the list of smiles box in Swiss ADME and run the process. From that we come to know the molecular weight, acceptors and donors and log p values etc…By using Protein data bank (PDB) we got a PDB ID for CDK 2 protein i.e. 5NEV. Later 3d ligand binding site and active site prediction for protein was identified. Total ligands used here are 5 and they are Calotropagenin, Anthraquinone, Flavanoid (Ternatin), Coumarin and Cannogenin. Then all the ligands were cleaned using Marvin sketch. Energy minimization of protein was done by using Swiss PDB viewer and then the Pyrx tool (Visualization tool) was used to check the least binding affinity of the ligands. From the 5 ligands one which has least binding affinity is taken for the docking process. Here the ligand which is having least binding affinity is Anthraquinone which is bound to the CDK 2 protein. And later the Docking visualization was performed using Biovia Discovery studio and Autodock tools-1.5.6.
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Keywords: Cyclin Dependent Kinase 2 protein, Anthraquinone, Lipinski rule, Ramachandran plot, Anticancer activity
n[if 424 equals=”Regular Issue”][This article belongs to International Journal of Biochemistry and Biomolecule Research(ijbbr)]
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References
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1.Yan Li Jingxiao Zhang et.al; 2015, Insights on Structural characteristics and ligand binding mechanism of CDK 2, International Journal of Molecular Science 2015. 2.Isabella A. Guedes, Camila S. De Magalhaes et.al;2013 Receptor-ligand molecular docking, 21 December 2013. 3.Shovonlal Bhowmick, Nora Abdulla Alfaris et.al;2020 Screening and Analysis of Bioactive food compounds for modulating the CDK 2 protein for cell cycle arrest: Multi-cheminformatics approaches for Anticancer therapeutics, Journal of Molecular structure, 15 September 2020. 4.Greg T. Hermanson, 2013, Bioconjugate Techniques, The reaction of Bioconjugation, 2013. 5.A.N Panche, A.D Deewan et al; Flavonoids: An Overview Journal of Nutritional Science, 5 article no.e47 https://doi.org.//10.1017/jns.2016.41 6.Aoife Lacy and Richard O Kennedy, Studies on Coumarins-related compounds to determine their therapeutic role in the treatment of Cancer, 2004. 7.Atef Gobran Hanna, Nagwa M.M Shalaby et.al; 2002, Structure of a Calotropagenin-derived from Calotropis procera July 2002. 8.Bhagat Madhulika and Sharma Vikas, Anti-cancer activity of Arka (Calotropis procera) on HCT- 15 cancer cell line, International Journal of Medical Sciences, 2010. 9.Seetharamaiah Nalini, Seetharamaiah Nandini et al; 2016, An electrochemical perspective assay for anticancer activity of Calotropis procera against glioblastoma cell line using carbon nanotubes- graphenes nano-conglomerate as a podium, 10 June 2016. 10.Tenzin Choedon, Ganeshan Mathan and Vijay Kumar, Anticancer and cytotoxic properties of the latex of Calotropis procera in a transgenic mouse model of hepatocellular carcinoma, World Journal of Gastroenterology (WJG) 2006 April 28;12(16): 2517-2522 Published online 2006 Apr28.Doi: 10.3748/wjg.v12.i16.2517 11.Mohammed A.M Al-Qah tani, Mohammad Abul Farah et.al; 2020, Anticancer effects of Calotropis procera latex extract in mcf-7 breast cancer cells, 2020. 12.Puja Tripathi, Subhasis Ghosh et.al; 2019, Bioavailability prediction of phytochemicals present in Calotropis procera by using Swiss ADME tool, 22 June 2019.
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International Journal of Biochemistry and Biomolecule Research
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| Volume | 02 | |
| [if 424 equals=”Regular Issue”]Issue[/if 424][if 424 equals=”Special Issue”]Special Issue[/if 424] [if 424 equals=”Conference”][/if 424] | 01 | |
| Received | May 9, 2024 | |
| Accepted | May 27, 2024 | |
| Published | August 23, 2024 |
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