Krithika Vasanth Naik,
Nilofar Khan,
- Research Intern BioNome for Genomics and Bioinformatics Solution, Bengaluru India
- Research Intern BioNome for Genomics and Bioinformatics Solution, Bengaluru India
Abstract
Cyclin 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.
Keywords: Cyclin Dependent Kinase 2 protein, Anthraquinone, Lipinski rule, Ramachandran plot, Anticancer activity
[This article belongs to International Journal of Biochemistry and Biomolecule Research(ijbbr)]
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References
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| Volume | 02 |
| Issue | 01 |
| Received | May 9, 2024 |
| Accepted | May 27, 2024 |
| Published | August 23, 2024 |