A Taxonomy for Drugs: 1 - Drug Class



It is intuitive to describe what a drug is in natural language - a small molecule, etc, but one problem is that these descriptive terms are context dependent, loosely defined and are used very variably across the literature; and so when someone asks 'How many small molecule drugs there are?' - first of all it depends on what is a 'drug', and secondly what is a 'small molecule'. As far as I can tell there is not a descriptive taxonomy for drugs (I use the term taxonomy here as a bridge term between a controlled vocabulary/dictionary and an ontology). For our own purposes within ChEMBL we need such a taxonomy, but post our initial thoughts here for comment, and no doubt (and hopefully), significant correction and improvement (use the comment section of the blog, then everyone can see any discussions).

Drugs are regulated products that are 'intended use in the diagnosis, cure, mitigation, treatment or prevention of disease' - let's not visit what a disease is, but move swiftly on to trying to sub divide this into obvious and useful categories/classes when thinking about molecular drug structures.

So for a Drug_Class, categorisation into the following seems intuitive and useful. Most of the action in drug discovery will be connected to the "Therapeutic" class.
  • Therapeutic - A substance with a curative action on a disease.
  • Supplement - A substance, used to address a deficiency of that substance (or of that substances normal function).
  • Imaging Agent - A substance used to image a molecule or structure within the body.
  • Diagnostic Agent - A substance used in the diagnosis of a disease, not involving imaging.
  • Other - A substance not covered by the categories above.
Drugs are then typically divided into Drug_Types - small molecules and biologicals.
  • Small Molecule - A substance with a molecular weight less than 1500 Da that is otherwise not a Biological.
  • Biological - A substance primarily composed from monomers of naturally occuring substances (e.g. amino-acids, sugars, nucleotides, etc.).
  • Other - A substance not covered by the categories above.
I hate these sort of self referential/recursive definitions, but please mail improvements! Within each of these two main classes there are some relevant, pragmatic and useful subdivisions - Drug_Type_Subclass.

For Small Molecules:
  • Inorganic - A non-organic substance.
  • Natural Product-derived - A substance that is derived from a naturally occurring primary or secondary metabolite.
  • Synthetic - An organic substance that is not derived from a naturally occurring priamry or secondary metabolite.
  • Other - A substance that is a Small Molecule which is not covered by the categories above.
For Biologicals:
  • Monoclonal antibody (mAb) - A substance similar in sequence to an antibody sequence.
  • Vaccine - A substance that acts through eliciting an acquired immune response in the patient.
  • Enzyme - A substance acting as a catalyst for a chemical reaction.
  • Virus - A substance with the biological characteristics of a competant virus.
  • Cell - A substance with the biological characteristics of a competant cell.
  • Peptide - A substance which is a polymer built primarily from amino acids, containing between two and twenty amino acids.
  • Protein - A substance which is a polymer built primarily from amino acids, containing in excess of twenty amino acids, and that is not a monoclonal antibody.
  • Oligosaccharide - A substance which is a polymer built primarily from sugar-like monomers.
  • Oligonucleotide - A substance which is a polymer built primarily from nucleotide-like monomers.
  • Other - A substance which is not covered by the categories above.
So, a consistent, semantically useful description of a specific drug is constructed from a combination of Drug_Type_Subclass, Drug_Type, and Drug_Class.

For example:

Sildenafil is a "synthetic small molecule therapeutic"
Abciximab is a "monoclonal antibody biological therapeutic".
Vitamin D3 is a "natural product-derived small molecule supplement".
Ioflupane 123I is a "synthetic small molecule imaging agent"

 Any feedback, pointers to any existing classifications/taxonomies, etc. would be very welcome.

Parts 2, 3 and 4 for this Drug taxonomy will be posted shortly.