Nature and purpose of this database

AntibioticDB is an open-access database that catalogues and describes known antibacterial agents, consolidating data from diverse sources that include the primary research literature, patents and conference abstracts.

AntibioticDB is based upon an idea by Professor Laura Piddock, who also designed and developed it, as described in Farrell et al. Initial development and curation of AntibioticDB was supported by the British Society for Antimicrobial Chemotherapy (March 2017 to June 2019) and curation led by Laura Piddock. Since 2022, further evolution of the AntibioticDB database and website has been led by GARDP, with curation overseen by Professor Alex O’Neill (University of Leeds, UK).

The information provided in AntibioticDB intends to serve both as a reference and a source of starting points for future research and (re-)development of antibacterial therapeutics. Within its 3000+ entries, AntibioticDB not only captures compounds that have reached preclinical/ clinical development or are licensed for clinical use, but also includes experimental antibacterial agents. Whilst many entries in AntibioticDB are classical ‘antibiotics’ (small molecules that directly inhibit or kill bacteria), the database also includes a diverse range of non-canonical antibacterial agents (e.g., anti-virulence compounds, antibodies, bacteriophages, host-directed agents).

Using the database

Searching the database

1. Type your query into the search bar and click ‘search’ (or hit Enter).
   • Type part of the name and add a * (asterisk sign) as the wildcard character.
   • Type only * and search for all compounds.
2. By default, searches are restricted to compound (drug) names, classes and synonyms. Select the 'search all database fields' option to search across all database fields.
3. Search results can be reordered, filtered or downloaded by selecting the corresponding options at the top of the table of results.
4. Click on an individual result to access all information held for that entry in AntibioticDB.
5. The entire current dataset in AntibioticDB can be viewed or downloaded from the landing page by clicking on “List or download”.

Chemical structure search

Search for compounds by chemical structure. Performs substructure, SMARTS, similarity and identity (exact) searches.

• Substructure: This search uses the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/) algorithm to match a drawn 2D structure and returns any compounds which contain the query structure.
• Similarity: Similarity search uses the Tanimoto coefficient to compare the similarity between the query molecule and molecules in the database using Pinpoint generated expanded fingerprints and returning all molecules above a user selected threshold (>70% or 85%).
  Please note: if your similarity search does not return appropriate results please try using the substructure function. (We are currently working on optimising our similarity search.)
• Exact: Exact match query returns all compounds matching the canonical SMILES, with no regards to the chiral specification. This is attained by Tanimoto comparison of fingerprints and returning all with 100% similarity.

1. Either: enter a SMILES representation of the chemical structure into the text box and press 'Import SMILES' to load the structure into the editor.
2. Or: draw the chemical structure into the editor. The icon in the top right above the atoms can be used to add other atoms and R groups.
3. Choose the type of search to perform from the drop-down menu on the top right (e.g. similarity - high).
4. Choose the type of chemical class to search for (as of Dec 2025 small molecules is the default and only option).
5. The returned structures are roughly ordered according to their flexibility/complexity.
6. On the results page, clicking on a compound's image or name will take you to its compound page. Clicking on the 'Use in search' button will load the compound into the editor so it can be modified if required and used in a further search.

1. Currently the search function does not consider chiral specification of matched compounds. This is to ensure that all relevant results will be returned. Please ensure that your input structure does not include chiral or isotopic specification, otherwise exact match and substructure may miss relevant structures.
2. Exact match and substructure searches are currently not able to recognise alternative tautomers that may be in the database. Please use similarity searching if you suspect this could be occurring.

How to cite AntibioticDB​​

L J Farrell, R Lo, J J Wanford, A Jenkins, A Maxwell, L J V Piddock (2018). Revitalizing the drug pipeline: AntibioticDB, an open access database to aid antibacterial research and development, Journal of Antimicrobial Chemotherapy, 73: 2284–2297, https://doi.org/10.1093/jac/dky208​​​

Further Resources​

Classes of antibiotics

Find more open-access resources about antimicrobial R&D, such as webinars, articles and more, on GARDP’s REVIVE. ​​