Hello, I've recently started exploring molecular docking applications, and I'm still in the early stages.I'd like to ask which proteins should be considered when examining the antimicrobial effects of certain molecules.
Is there a list of these proteins(that I should use as a docking protein), or are there general rules for proteins that should definitely be examined?
Also, can I perform docking not with a molecule but directly with an organism? If so, what should I look for to predict antimicrobial effects?
Could you please guide me on this?
Thank you.
it's important to consider specific proteins that play crucial roles in the survival and reproduction of microorganisms. Enzymes involved in cell wall synthesis: Proteins like penicillin-binding proteins (PBPs) are crucial for bacterial cell wall formation.
DNA gyrase and topoisomerases: Involved in DNA replication and repair, these are essential targets for antimicrobial compounds.
Ribosomal proteins: Targeting bacterial ribosomes can disrupt protein synthesis. Utilize databases like the Protein Data Bank (PDB) to find crystal structures of your selected proteins. Molecular docking predictions should be validated through in vitro and in vivo experiments.for in vitro evaluation you can use microorganisms directly.
Some general guidelines and considerations:
1. Target Organism: Determine the specific microorganism(s) you want to investigate. This could be a particular bacterium, virus, fungus, or other pathogen. The choice of proteins for docking will depend on the biology and characteristics of the target organism.
2. Protein Targets: Identify key proteins or biomolecules that play crucial roles in the survival, replication, or virulence of the target organism. These proteins are potential targets for antimicrobial agents. Examples of common protein targets include enzymes, receptors, transporters, and structural proteins.
3. Literature Review: Conduct a literature review to identify proteins that have been previously studied and validated as potential targets for antimicrobial agents against your target organism. Published research articles, reviews, and databases such as the Protein Data Bank (PDB) can provide valuable information on known protein targets.
4. Drug Targets Databases: Explore specialized databases that provide information on potential drug targets for various microorganisms. Examples include the DrugBank database (https://www.drugbank.ca/) and the Comprehensive Antibiotic Resistance Database (CARD) (https://card.mcmaster.ca/).
5. Protein Structure Availability: Check if the three-dimensional structures of the proteins of interest are available in the Protein Data Bank (PDB) or other protein structure databases. Having experimentally determined structures will facilitate molecular docking studies.
Regarding your question about performing docking with an organism rather than a molecule, it is not common to perform docking directly with an entire organism. Molecular docking typically involves studying the interaction between a small molecule (ligand) and a specific protein target. However, you can consider the organism's proteins as potential docking targets.
To predict antimicrobial effects, you can focus on the binding affinity and interaction between the ligand and the protein target. A strong and specific binding interaction can suggest potential antimicrobial activity. Additionally, you can consider factors such as the ligand's ability to disrupt essential biological processes, inhibit enzymatic activity, or interfere with protein-protein interactions.
Good luck: partial credit AI
Hi! As suggests before, it's not a common procedure to perform a docking with entire organisms; also it quite complicated because you need a huge computational power.
Usually the most affordable and reliable dockings are protein-small ligand (antibody, DNA, RNA)
Protein is prime structure needed for docking while microorganisms have protein, circular DNA and RNA as well. It won't be easy to perform docking for whole organism. It could be perform if all the protein listed alongwith the PDB IDs.
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