Chemical space refers to the entire set of possible stable chemical compounds, real or hypothetical, that can exist within defined rules of chemistry. Each compound can be represented as a point in a multi-dimensional space defined by molecular descriptors such as structural (e.g., size, shape, functional groups, and connectivity) stereochemistry and physicochemical properties (e.g., molecular weight, polarity, lipophilicity, hydrogen-bonding capacity, and charge distribution).
The concept is central to drug discovery, as it provides a framework for mapping and exploring large set of possible molecules, including those not yet synthesized and tested, thereby guiding the identification of molecules for biological testing.
The chemical space of antibiotics is a relatively narrow region within this broader space. Clinically useful antibiotics tend to cluster around certain structural features and physicochemical properties that enable them to enter bacterial cells and bind to specific targets. Many existing antibiotics share common scaffolds, which has contributed to repeated rediscovery of similar compounds Expanding the antibiotic chemical space—through approaches such as fragment-based design, diversity-oriented synthesis, mining natural product biosynthetic gene clusters, and other strategies—is seen as essential for identifying new classes of antimicrobials and addressing the challenge of resistance.