Two‐ and Three‐dimensional Rings in Drugs

TLDR

Fragment‑based drug discovery commonly uses small, flat aromatic rings, but growing interest in novel chemical space and synthetic accessibility has increased focus on 3D fragments. The study analyzes 3D and 2D ring fragments in marketed drugs. The authors evaluated ring assemblies, molecular shapes, and target‑class relationships to assess 3D versus 2D fragments. The analysis reveals that 3D ring systems exhibit high structural and shape diversity and differ markedly from 2D fragments in ligands targeting GPCRs, ion channels, and enzymes.

Abstract

Using small, flat aromatic rings as components of fragments or molecules is a common practice in fragment‐based drug discovery and lead optimization. With an increasing focus on the exploration of novel biological and chemical space, and their improved synthetic accessibility, 3D fragments are attracting increasing interest. This study presents a detailed analysis of 3D and 2D ring fragments in marketed drugs. Several measures of properties were used, such as the type of ring assemblies and molecular shapes. The study also took into account the relationship between protein classes targeted by each ring fragment, providing target‐specific information. The analysis shows the high structural and shape diversity of 3D ring systems and their importance in bioactive compounds. Major differences in 2D and 3D fragments are apparent in ligands that bind to the major drug targets such as GPCR s, ion channels, and enzymes.