Bridging the gap between small molecule and biologics editing
An increasing number of new FDA approved drugs are biologics; in 2015 alone, 19 out of the 51 approved drugs were biological entities. Increasingly, the development of these complex drugs requires chemists and biologists to collaborate closely from ideation to product maturity. During this process candidate molecules undergo iterative changes which need to be communicated precisely and unambiguously to all researchers involved in the project. Although the cheminformatics world is well covered in terms of software to draw, store, search, report and manage small molecules, there is currently no efficient way to handle biological entities in the same manner.
ChemAxon, a well-known cheminformatics software provider, recognized and bridged this information gap between biology and chemistry by the development and integration of Biomolecule Toolkit and the biological editor, BioEddie. We provide unambiguous representation for biologics: peptides, oligonucleotides, proteins, antibodies, antibody drug conjugates etc., including those containing unnatural and chemically-modified components with the ability to define ambiguous structural elements. The standardized representation, paired with the ability to round-trip between standard chemical and biological file formats (MDL MOL to HELM conversion and vice versa), allows researchers to keep a single data store of molecular assets (Biomolecule Toolkit), in which they can query based on sequences, chemical structure or metadata. Relevant molecules can be exported for further processing in other computational tools. In this poster, we will demonstrate the novelty of our approach and present a couple of case studies: one for CHEMBL v21 peptides dataset and one for antibody registration.