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I have studied a paper that constructs the pathway fingerprint of a drug, which has a vector of $0$ and $1$, and they compare the pathway fingerprint using a similarity measure to assess how similar the drugs are.

But I don't know where can I download pathways and how to generate their fingerprint vector to evaluate them. I checked KEGG website but could not find anything there to download. The paper can be downloaded from: https://pubmed.ncbi.nlm.nih.gov/22426982/

I really appreciate answers that can help me to solve the problem.

Update Since i am not familiar with DrugBank and biology science, when I parsed the xml file of drugbank, I find a tag with name pathway . But i am not sure that do these elements show the pathway of drug or not? Is it possible to use them to construct the pathway fingerprint vector for drugs? what does <uniprot-id>P00734</uniprot-id> mean?

this is the content of pathway tag for Lepirudin:

<pathways>
    <pathway>
      <smpdb-id>SMP0000278</smpdb-id>
      <name>Lepirudin Action Pathway</name>
      <category>drug_action</category>
      <drugs>
        <drug>
          <drugbank-id>DB00001</drugbank-id>
          <name>Lepirudin</name>
        </drug>
        <drug>
          <drugbank-id>DB01022</drugbank-id>
          <name>Phylloquinone</name>
        </drug>
        <drug>
          <drugbank-id>DB01373</drugbank-id>
          <name>Calcium</name>
        </drug>
      </drugs>
      <enzymes>
        <uniprot-id>P00734</uniprot-id>
        <uniprot-id>P00748</uniprot-id>
        <uniprot-id>P02452</uniprot-id>
        <uniprot-id>P03952</uniprot-id>
        <uniprot-id>P03951</uniprot-id>
        <uniprot-id>P00740</uniprot-id>
        <uniprot-id>P00451</uniprot-id>
        <uniprot-id>P12259</uniprot-id>
        <uniprot-id>P00742</uniprot-id>
        <uniprot-id>P02671</uniprot-id>
        <uniprot-id>P02675</uniprot-id>
        <uniprot-id>P02679</uniprot-id>
        <uniprot-id>P00488</uniprot-id>
        <uniprot-id>P05160</uniprot-id>
        <uniprot-id>P00747</uniprot-id>
        <uniprot-id>P00750</uniprot-id>
        <uniprot-id>P08709</uniprot-id>
        <uniprot-id>P13726</uniprot-id>
        <uniprot-id>Q9BQB6</uniprot-id>
        <uniprot-id>P38435</uniprot-id>
      </enzymes>
    </pathway>
  </pathways>

```
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1 Answer 1

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I know nothing about drug databases, but am familiar with Kegg. As far as I can see from the paper (and I may be wrong) The drug target database would contain the names of enzymes, the activity of which is affected by drugs. So the problem would seem to be to identify so-called Kegg ‘pathways’ in which these target enzymes occur.

(I use the adjective “so-called” as Kegg pathways are not generally what a biochemist would regard as a pathway, but areas of metabolism. However this would not matter if all one is trying to do is find a correlation.)

The poster would seem, therefore, to need to download a list of enzymes for each Kegg pathway. At one time all the Kegg information was available free of charge (I downloaded a considerable amount — although not the enzymes — to construct a relational database). However now one needs to purchase a license to do this — presumably what the authors of the paper did — at a cost of over $1000 pa.

Unless one has grant funding or is independently wealthy, it would seem to be necessary to explore alternatives, such as MetaCyc (https://metacyc.org).

Postscript The addendum from the poster shows the UniProt IDs for the targets of the drug. These can be converted to Kegg IDs using the conversion tool on the Kegg site (https://www.genome.jp/kegg/tool/conv_id.html). The XML tag entitled “pathway” is not equivalent to a Kegg metabolic pathway as such, although the example seems to consist of proteins involved in blood clotting. If my interpretation is correct, it would be irrelevant to the procedure I suggest. However the original paper is sufficiently vague that I cannot be sure.

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  • $\begingroup$ Thanks for your reply and your information. I added a new update section to my question which shows a tag wit name pathway in xml file of drugbank. does show the desired pathway of the drug? $\endgroup$
    – Orca
    Commented Aug 15, 2023 at 10:07
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    $\begingroup$ @Orca — I've added a PS. If I were you I'd email the authors of the paper. $\endgroup$
    – David
    Commented Aug 17, 2023 at 22:22
  • $\begingroup$ thanks for the time you spent on my question. the answers did not solve my problem, but a appreciate it with upvote $\endgroup$
    – Orca
    Commented Aug 23, 2023 at 11:27

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