Notation

This package is able to convert a special form of IUPAC strings for glycans into SMILES strings. To convert normal IUPAC notation for organic molecules into SMILES there are several tools already published, e.g., OPSIN <https://opsin.ch.cam.ac.uk/>.

Short Overview

In the following, we will show four different ways to describe lactose, a disaccharide of D-Galactose and D-Glucose connected with a 1-4 beta-O-glycosidic bond as shown in the image beyond.

• IUPAC:

  beta-D-galacto-hexopyranosyl-(1->4)-beta-D-gluco-hexopyranose

• IUPAC-condensed:

  Gal(b1-4)Glc b

• IUPAC-full:

  Galp(b1-4)Glcpb

• IUPAC-simplified:

  Galb4Glc b

All four notations describe the same molecule. For the standard IUPAC, there are published tools available. For the other three, we developed this tool. For the sake of simplicity, we will only describe IUPAC-condensed here. The other two IUPAC derivates can be derived by either giving all information on the glycans (full) or by reducing the bond description to the absolute minimum (simplified).

IUPAC-condensed

The IUPAC-condensed notation of glycans is the most commonly used notation in publications, databases, and other sources. Its wide usage is due to the compact descriptions of glycans and the human-readability of the notation.

This notation is a specialized form of the general IUPAC notation that is used to describe other organic molecules in a standardized way. It is specifically suited for glycans and their variability in structure and attached functional groups. It is capable of representing these structures in a compact and human-readable form.

Chains

Glycans have a complex, yet regular, structure, especially when described using the IUPAC notation. For example, Man(a1-4)Man(a1-4)Man(a1-4)Man is a simple chain of four mannopyranose monosaccharides connected with 1-4 alpha-O-glycosidic bonds. Important to note is that the root of the glycan tree is always the last monosaccharide in an IUPAC formula. The chain grows from the end by prepending elements like verb+Man(a1-4)+, which corresponds to adding a new mannose to a leaf-monomer of the glycan.

Branches

The branching of the trees is described by introducing the new branch in square brackets. For example, Man(a1-4)Man(a1-3)[Man(a1-4)Man(a1-4)]Man(a1-4)Man is a tree of mannopyranoses that has two monosaccharides before splitting into two chains with again two mannopyranoses each. The branching is put right in front of the monomer where the root of the side branch is bound to the main strand.

Even more branches

This can be extended to three chains of two monosaccharides each bound to a single mannopyranose Man(a1-4)Man(a1-2)[Man(a1-4)Man(a1-3)][Man(a1-4)Man(a1-4)]Man

Attachments, a.k.a functional groups

Modifications in IUPAC are directly annotated at the modified monosaccharide. The annotation is often done by first naming the position at which carbon atom a functional group is attached. Then, an abbreviation of that group is given. So, Man3S describes a mannose with a sulfate attached to the third carbon atom. The number can also be dropped in case of a functional group attached to a standard position, as in GalNAc where an acetamid-group is attached to the second carbon atom of galactopyranose. There are also other possibilities to denote a functional group but that is beyond the scope of this introduction.

Variety of Attachments

Modifications of glycans include added sulfur groups (Man3S), added phosphate groups (Man3P), added amine groups (ManN), and many more. Functional groups can be attached to any oxygen, nitrogen, or a carbon atom in the monosaccharide (e.g., Man4S, Man4P, or ManNS). Additionally, one can combine them in any way (e.g., Man3S4P). The only restriction is that one cannot put two modifications to the same atom (e.g., Man2S2P).