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Updated: May 12, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Druggable chemical space and enumerative combinatorics.

¹Eisai Inc,, 4 Corporate, Dr, Andover, MA, 01810, USA. melvin_yu@eisai.com.

Journal of Cheminformatics

|April 19, 2013

Summary

This summary is machine-generated.

Enumerative combinatorics generated novel virtual compounds with drug-like properties and unique ring structures. These compounds expand chemical space and could inspire new drug scaffold design for high-throughput screening (HTS).

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High-throughput Identification of Synergistic Drug Combinations by the Overlap2 Method

High-throughput Identification of Synergistic Drug Combinations by the Overlap² Method

Published on: May 21, 2018

Area of Science:

Computational chemistry
Medicinal chemistry
Drug discovery

Background:

Marketed drugs, drug-likeness, and chemical space are extensively studied.
Enumerative combinatorics offers a method for designing novel compounds.
This approach can enhance high-throughput screening (HTS) libraries.

Purpose of the Study:

To explore the utility of enumerative combinatorics in designing novel chemical structures.
To assess the drug-like properties and chemical space coverage of computationally generated compounds.
To determine the potential of these virtual compounds in drug discovery.

Main Methods:

Utilized enumerative combinatorics with simple atomic components (C, H, N, O) to generate virtual compounds.
Incorporated ring formation capabilities without molecular weight constraints.
Compared generated compounds against existing databases (ChEMBL_14, MDDR, Drug Bank, Dictionary of Natural Products) using Tanimoto index (ECFP_4).

Main Results:

Virtual compounds exhibited bulk physicochemical properties associated with drugs.
Ring assemblies of virtual compounds occupied novel or under-represented areas of chemical shape space.
Up to 0.21% of virtual compounds had a Tanimoto index of 1.0 (ECFP_4), potentially reflecting a true hit rate in experimental HTS.

Conclusions:

Enumerative combinatorics yields virtual compounds with drug-like characteristics and unique ring assemblies.
These novel structures occupy unexplored regions of chemical shape space.
The derived structures serve as unbiased starting points for designing novel drug scaffolds.