Sugar & Splice

Cheminformatics of oligopeptides, oligosaccharides and oligonucleotides

Biological macromolecules, such as peptides, proteins, RNA aptamers, carbohydrates and drug-antibody conjugates, pose unique challenges that stretch typical cheminformatics systems to their limits. Not only their size, but also their complexity and repeated substructures, make many of the standard approaches used for small molecules, such as fingerprint-based similarity or all-atom 2D co-ordinate depiction inappropriate for these classes of compounds. As a result, pharmaceutical and biotechnology companies working with biologics often different registration, compound management, ELN and analysis systems to those used for small molecule chemistry.

NextMove Software's Sugar & Splice toolkit and suite of tools are designed to bridge the gulf between cheminformatics and bioinformatics by providing functionality for seamlessly integrating the representations used in each domain. All-atom representations such as SMILES or MOL can be converted to IUPAC condensed line-notations or sequences (and vice versa). Non-standard residues are supported and the list can be extended by the user. This approach allows BLAST searching and sequence alignment of a chemical database stored as SMILES or MDL connection tables, or SMARTS substructure searching of protein databases, including non-standard amino acids and post-translational modifications.

Sugar & Splice allows supports the generation of depictions based on IUPAC (Fig. 1) or FDA recommendations for peptides, and the SNFG guidelines for sugars.

Figure 1. Sugar & Splice depiction of Iturelix given its SMILES string as input

• A presentation describing the combination of LeadMine and Sugar & Splice to identify and extract peptides from PubMed Abstracts presented at the ACS meeting in Boston, August 2018 [PDF]
• A presentation describing the use of Sugar & Splice to identify and analyse biologics in PubChem presented at the ACS meeting in Washington DC, August 2017 [PDF]
• A presentation describing Sugar & Splice's naming of named peptide derivatives presented at the ACS meeting in Boston, August 2015 [PDF]
• A presentation describing Sugar & Splice's naming of unusual backbones and sidechain bridges presented at the ACS meeting in San Francisco, August 2014 [PDF]
• A presentation describing Sugar & Splice's naming of non-standard amino acids presented at the ACS meeting in Dallas, March 2014 [PDF]
• A presentation describing Sugar & Splice presented at the American Chemical Society (ACS) National Meeting in New Orleans, April 2013 [PDF]
• A presentation describing Sugar & Splice's peptide perception and depiction presented at the American Chemical Society (ACS) National Meeting in San Diego, March 2012 [PDF]