The ChEMBL-og

There is an excellent description of specific subtypes of monoclonal antibodies on Wikipedia, these can be easily incorporated into the Drug_Class section of our drug taxonomy. Specifically as Drug_Type_Subsubclass. An interesting property of this classification is that it should be possible to write an algorithm that classifies arbitrary sequences against this taxonomy. mab - whole monoclonal antibody. Fab - fragment, antigen-binding (one arm). F(ab')2 - fragment, antigen-binding, including hinge region (both arms). Fab' - fragment, antigen-binding, including hinge region (one arm). scFv - single-chain variable fragment. di-scFv - dimeric single-chain variable fragment. sdAb - single-domain antibody. 3funct - trifunctional antibody. BiTE - bi-specific T-cell engager. Other - an antibody like drug that does not fit one of the above classes.

The next area for consideration in our descriptive taxonomy for drugs is stereochemistry . There are many differing types of stereoisomers encountered in general chemistry, and the area is complex, but the majority of these are not relevant for drug discovery; for example atropisomers , although an important effect is not important for among drug substances. The most significant category of stereochemistry for drug like molecules involves chiral centers at sp 3 hybridised carbon atoms connected to four chemically distinct atoms (often giving rise to  enantiomerism ). Another relevant case of stereoisomerism for drugs are  diastereoisomers , these are stereoisomers that are not enantiomers, and include cis -/ trans - ( E -/ Z -) configuration of alkenes. So for Drug_Stereochemistry_Class , a drug can be: Chiral - containing a single defined stereoisomer of the drug substance, and which lacks an internal plane of symmetry. Racemic - containing a mixture of stereoisomers...

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 ...