SpotRM Web Help

SpotRM is an easy to use and understand web application.

You search either by structure or text. A structure search will highlight a potential reactive metabolite alert in the searched structure while a text search will list drugs associated with your text string (more below). To have an understanding of the basic concepts, we recommend reading of our perspective paper: A. Claesson & A. Minidis, Chem. Res. Toxicol. 2018. Also reading the Scope text helps to understand the selection and inclusion/exclusion of drugs and data; these texts also explain the advantages and limitations of using SMARTS as descriptions of RM alerts. A list of the abbreviations used in the monographs and MiCs can be found here.

We strongly recommend that users set their web browser to open pdf files (i.e. monographs and MiCs) in the browser and not in a separate application; otherwise links in these files to other PDFs will not open.

Structure Search

Input:

Structures may be sketched with JSME, a free molecular editor by Bruno Bienfait and Peter Ertl J. Cheminformatics 2013, 5:24. Aside from drawing, you can paste structures as smiles, mol or sdf. If needed, visit their documentation at JSME Help pages.

You can paste a SMILES or InChI string into the marked window. You can also upload files in the formats *.smi, *.sd, and *.sdf, which are automatically recognized. In a file with SMILES strings you can have a name attached, for example a SMILES file can have:

Just SMILES, one per line,
A SMILES followed by a compound name separated by a single whitespace character, in which case the compound name is used in the output. Note that white space characters are not allowed in compound names. An example line could be:
CCN(CC)CCNC(=O)C1=C(NC(=C1C)C=C2C3=C(C=CC(=C3)F)NC2=O)C Sunitinib
A SMILES followed by a name followed by one or more data fields all separated by single whitespace characters. In this case the name is used and all subsequent fields dropped,
An optional header line of any format.

If you do not have any SMILES directly available, here are a few that you can copy and test:

CCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)Br)O)Br
CCCN(CCC1=CC=CS1)C2CCC3=C(C2)C=CC=C3O
CCN(CC)CCNC(=O)C1=C(NC(=C1C)C=C2C3=C(C=CC(=C3)F)NC2=O)C sunitinib

And here are a couple of InChI strings:

InChI=1S/C17H12Br2O3/c1-2-13-15(10-5-3-4-6-14(10)22-13)16(20)9-7-11(18)17(21)12(19)8-9/h3-8,21H,2H2,1H3
InChI=1S/C15H13ClFNO2/c1-9-5-6-13(10(7-9)8-14(19)20)18-15-11(16)3-2-4-12(15)17/h2-7,18H,8H2,1H3,(H,19,20)

Output

The input structures are listed to the right in in a table with alert hits highlighted (picture below). Clicking a drug name gives its structure as a pop-up. Alerts for each input structure are listed in Severity order (see Scope for an explanation of this concept) and a sum of these scores is listed in the header.

Text search

Text search covers:

Drug names in the database. You can get a full listing of all 317+ drugs in the database by querying asterisk with an (⁎).
Useful keywords listed in a PDF_text field: for example many pharmacological indications and mechanisms like antiepileptic, NSAID, antifungal, and analgesic etc. Important chemical groups, e.g. hydrazine, thiourea and lactam, can also be found there.
Chemical names and known synonyms
Market Status

Names of structural alerts are currently not searchable

Output

Output is in a table based on drug names

If you do not find an answer to your question you should send it to ✉ support and you are also welcome with suggestions for improvements.

REST API Searches

SpotRM also has a REST API which allows one to run searches from scripting environments such as python or Knime, or to integrate access to the SpotRM functionality into your inhouse systems. Several examples can be found here, including one showing how to retrieve a listing of all the available endpoints, and should show you enough of the API to get started with your own scripts or integration. Note that an active account is required to access the SpotRM API.

Acknowledgements

SpotRM Web depends on a number of open source components and libraries which are greatfully acknowledged and include:

RDKit: Open-source cheminformatics: http://www.rdkit.org (BSD-3 licence)
Python Flask: A lightweigh web application framework: https://palletsprojects.com/p/flask/ (BSD-3 licence)
JSME: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013) (BSD-3 licence)