I am currently doing a project on phytochemicals and its anti-cancer properties.
My question is actually in two parts:
Please provide detailed answers.
Thank you in advance.
1. Browse through available literature for cancer related proteins and search for its structure on the Protein Data Bank.
2. Here is a good series of tutorials for Autodock Vina
https://youtu.be/Sux91FJ3Xe8
1. try some receptors for docking: AKT, CKD6, HER2, MAPK
2. many tutorials using autodock vina on the youtube channel
The prime problem is to find out which proteins your compound does interact with. So you would probably first look at various chemical databases to find out if a) they contain your molecule (or a close relative) and
b) they contain annotations as to their interactions with potential target proteins and cellular functions.
You might also want to do a comprehensive literature search to find out which target proteins have been identified for your compound.
You best bets are Pubchem ( https://pubchem.ncbi.nlm.nih.gov ) and ChemSpider ( http://www.chemspider.com ), here is a more comprehensive list:
https://en.wikipedia.org/wiki/List_of_chemical_databases
If you succeed to find potential target proteins, you might want to look them up in UniProt (https://www.uniprot.org) for a concise summary of their functions and properties, and to get the sequences of these proteins.
Then you need to find out if structures of these target proteins are available in the PDB database of macromolecular structures ( https://www.rcsb.org ), best using a blast search with their sequence, to see whether any structure of these proteins are available, or at least structures of sufficiently close homologs that you can build reliable homology models (e.g. using SwissModel https://swissmodel.expasy.org )
Once you have identified potential targets, you can think of starting your docking, e.g. using autodock vina http://autodock.scripps.edu
Have you evaluated your molecules for anticancer activity (inhibition of cell proliferation using cancer cell lines) in-vitro. If yes, then find out through literature survey what receptors or proteins are over expressed in these cell lines which are contributing to uncontrolled proliferation. This is one of the ways you can select your targets for docking. First rule out that your phytochemicals do not have cytotoxicity.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides