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International Journal of Biochemistry and Biomolecule Research Original Research

Anticancer Activity of Calotropis procera by Molecular Docking Analysis

  1. Krithika Vasanth Naik BioNome for Genomics and Bioinformatics Solution, Bengaluru
  2. Nilofar Khan BioNome for Genomics and Bioinformatics Solution, Bengaluru

Abstract

Cyclin-dependent kinase 2 (CDK2) is a protein synthesized by Calotropis procera. It is known to be responsible for causing cancer in the human body. Studies have presented the significance of the phytochemicals to inhibit the CDK2 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 drug-likeness 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 ran the process. From that, we come to know the molecular weight, acceptors, donors log p values, etc. By using a protein data bank (PDB) we got a PDB ID for CDK2 protein, i.e., 5NEV. Later 3d ligand binding site and active site prediction for protein was identified. The total ligands used here are 5 and they are calotropagenin, anthraquinone, flavonoid (ternatin), coumarin, and cannogenin. Then all the ligands were cleaned using Marvin's sketch. Energy minimization of protein was done by using the 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 the 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 CDK2 protein. And later the docking visualization was performed using Biovia Discovery Studio and AutoDock Tools-1.5.6.

Keywords

References (12)

  1. Li Y, Zhang J, Gao W, Zhang L, Pan Y, Zhang S, et al. Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2. International Journal of Molecular Sciences. 2015;16(5):9314-9340. doi:10.3390/ijms16059314
  2. Guedes IA, de Magalhães CS, Dardenne LE. Receptor–ligand molecular docking. Biophysical Reviews. 2013;6(1):75-87. doi:10.1007/s12551-013-0130-2
  3. Bhowmick S, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, et al. Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: Multi-cheminformatics approaches for anticancer therapeutics. Journal of Molecular Structure. 2020;1216:128316. doi:10.1016/j.molstruc.2020.128316
  4. Bioconjugate Techniques. 2013. doi:10.1016/c2009-0-64240-9
  5. Panche AN, Diwan AD, Chandra SR. Flavonoids: an overview. Journal of Nutritional Science. 2016;5. doi:10.1017/jns.2016.41
  6. Lacy A. Studies on Coumarins and Coumarin-Related Compounds to Determine their Therapeutic Role in the Treatment of Cancer. Current Pharmaceutical Design. 2004;10(30):3797-3811. doi:10.2174/1381612043382693
  7. Hanna AG, Shalaby NMM, Morsy NAM, Simon A, Tóth G, Malik S, et al. Structure of a calotropagenin‐derived artifact from Calotropis procera. Magnetic Resonance in Chemistry. 2002;40(9):599-602. doi:10.1002/mrc.1057
  8. Madhulika B, Vikas S. Anticancer activity of Arka (Calotropis procera) on HCT-15 cancer cell line. Int J Med Sci. 2010;2(2):152–4.
  9. Nalini S, Nandini S, Shivappa Suresh G, Savio Melo J, E. Neelagund S, Nagaiah Naveen Kumar H, et al. An Electrochemical Perspective Assay For Anticancer Activity Of Calotropis Procera Against Glioblastoma Cell Line (LN-18) Using Carbon Nanotubes- Graphene Nano- Conglomerate As A Podium. Advanced Materials Letters. 2016;7(12):1003-1009. doi:10.5185/amlett.2016.6395
  10. Choedon T. Anticancer and cytotoxic properties of the latex of Calotropis procera in a transgenic mouse model of hepatocellular carcinoma. World Journal of Gastroenterology. 2006;12(16):2517. doi:10.3748/wjg.v12.i16.2517
  11. Farah M, M. Al-Qahtani M, Abou-Tarboush F, Al-Anazi K, Al-Harbi N, Ali M, et al. Anticancer effects of Calotropis procera latex extract in mcf-7 breast cancer cells. Pharmacognosy Magazine. 2020;16(71):550. doi:10.4103/pm.pm_156_20
  12. Tripathi P, Ghosh S, Talapatra SN. Bioavailability prediction of phytochemicals present in Calotropis procera (Aiton) R. Br. by using Swiss-ADME tool. World Sci News. 2019;131:147–63.