By subtractive genomics, I have obtained histidine-containing phosphocarrier protein (HPr) as one of the drug targets in a streptococcus strain. It is non-homologous to human proteome. Several literature infers that it can be a potent drug target. I have already performed virtual screening using approximately 1 million small molecules. For the purpose, I used AutoDock Vina for virtual screening placing grid center over Ser46, which is highly conserved in gram positive bacteria’s as stated by literature.
I want more bioinformatic ways to justify that it can be a better drug target, as I have a query - say the ligand may bind to HPr of other gram positive bacteria’s which are beneficial to humans.
Kindly discuss and suggest me some ideas.
The 1st question to ask is whether the protein is essential for the survival of the bacteria in vivo (or rich medium in vitro). In terms of bioinformatics, check among sequenced Strep strains for conservation of the residues in the ligand binding site. A high level of conservation is needed.
Dear Adam, it is an essential protein not only among streptococcus, but in almost all the bacterias. For the convenience, follow this link, which takes you to CDD of NCBI representing the target sequence HPr. There you can see, the conserved serine at 46 position saying regulatory phosphorylation site on conserved domain PTS-HPr, upon which the grid centre was placed while docking calculations.
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?SEQUENCE=YP_001450835.1&FULL
Based on the information given by you, I understand that you are targeting the sugar/carbohydrate metabolism in a streptococcus strain. If you have proved that HPr from your strain of streptococcus strain is not homologous to humans, then I think you can start checking if it is homologous or not homologous to other gram positive bacterias present in the human gut (or human microbiom) that are beneficial for human beings.
Although it would certainly be preferable for an antibacterial drug to have selectivity for the pathogen species over commensal bacteria of humans, this is not essential when saving the patient's life is at stake.
As I understand it, the conserved serine is the site of phosphorylation by a kinase. If the ability of this site to become phosphorylated is essential to the survival of the bacteria, then the serine kinase could be another good drug target.
On the other hand, if phosphorylation of this serine residue is not crucial to the function of the phosphotransferase system, then it might not be a good place to focus your virtual screening effort. The phosphoacceptor histidine site might be better, if it is suitable from a druggability perspective.
And have you considered attempting to interfere with the protein-protein interaction between HPr and its kinase?
Dear Kavisa, as you said to perform similarity search with other human beneficial gut organisms, Its difficult to get the list of such organisms, against which I can perform BLAST search...
And dear Adama I have performed STRING protein interaction analysis. Regarding this, I have attached the an image. I took sequences of all the proteins are involved in the PTS system of the organism (as analyzed by KEGG pathway database) and submitted it to STRING. Fascinatingly the protein HPr that I had targeted has the highest STRING score, and hence I considered it as a hub protein.
Here with I have attached few files
KEGG LINK TO THE PATHWAY:
http://www.genome.jp/dbget-bin/www_bget?pathway+sgo02060
File having all the 33 sequences that were submitted to STRING
If possible and you feel convenient, please submit the sequences again the sequences to STRING
and the STRING image that I have obtained.
That is true. At least if not all, the most well known (proven) bacterias can be considered to support your work. Then you can go for docking analysis for these well proven bacterial strains which are beneficial for human beings. As you have already screened 1 million small molecules, chose the best and screen the proteins in the good bacterias. If its specifically binds well to your drug target protein alone, then its worth a try to be taken forward, like in vitro analysis.
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