An algorithm to identify functional groups in organic molecules

Peter Ertl

doi:10.1186/s13321-017-0225-z

Abstract

BackgroundThe concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional groups are based on a predefined list of substructures. We are not aware of any program that can identify all functional groups in a molecule automatically. The algorithm presented in this article is an attempt to solve this scientific challenge.ResultsAn algorithm to identify functional groups in a molecule based on iterative marching through its atoms is described. The procedure is illustrated by extracting functional groups from the bioactive portion of the ChEMBL database, resulting in identification of 3080 unique functional groups.ConclusionsA new algorithm to identify all functional groups in organic molecules is presented. The algorithm is relatively simple and full details with examples are provided, therefore implementation in any cheminformatics toolkit should be relatively easy. The new method allows the analysis of functional groups in large chemical databases in a way that was not possible using previous approaches.Graphical abstract.

Highlights

The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and chemical nomenclature
The algorithm outlined above was implemented using the Novartis in-house cheminformatics system written in Java and was tested by identifying and collecting functional groups (FGs) for bioactive portion of the ChEMBL database [13], consisting of ~483,000 molecules with activity below 10 um on any ChEMBL target
A list of 768 FGs that are present in at least 10 ChEMBL molecules is provided in pseudo-SMILES notation as Additional file 1

Summary

Introduction

The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and chemical nomenclature. We are not aware of any program that can identify all functional groups in a molecule automatically. The concept of functional groups (FGs)—sets of connected atoms that determine properties and reactivity of parent molecule, forms a cornerstone of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and, last but not least, chemical nomenclature. The study of common FGs forms substantial part of basic organic chemistry curriculum. Numerous scientific papers and books focus on properties and reactivity of various FGs. A well known example is the classical book series “Chemistry of functional groups” describing various classes of organic molecules [1] consisting of over 100 volumes.

Methods

Results

Conclusion