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Related Experiment Video

Updated: Feb 8, 2026

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

Structural Insights on Fragment Binding Mode Conservation.

Malgorzata N Drwal¹, Guillaume Bret¹, Carlos Perez²

¹Laboratoire d'Innovation Thérapeutique , UMR7200, Université de Strasbourg , 74 Route du Rhin , 67401 Illkirch , France.

Journal of Medicinal Chemistry

|June 16, 2018

Summary

This summary is machine-generated.

Fragment binding modes are conserved when growing molecules, showing chemical changes are tolerated. Crystallized fragments effectively cover binding pockets for structure-based drug design.

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Area of Science:

Structural biology
Medicinal chemistry
Drug discovery

Background:

Understanding fragment binding is crucial for drug discovery.
Fragment-based drug design (FBDD) relies on conserved binding modes.

Purpose of the Study:

To analyze fragment and ligand binding modes in the Protein Data Bank.
To provide experimental evidence for binding mode conservation during molecular growth.
To assess binding pocket coverage by crystallized fragments.

Main Methods:

Large-scale analysis of the Protein Data Bank (PDB).
Comparison of binding modes for 1832 drug-like ligands and 1079 fragments across 235 proteins.
Analysis of crystallization additives for structure-based drug design relevance.

Main Results:

Fragment and drug-like superstructure binding modes are largely conserved on the same protein.
Small chemical modifications to fragments typically do not alter binding modes, barring conformational changes.
Sufficiently crystallized fragments achieve good interaction coverage of protein binding pockets.

Conclusions:

Fragment binding modes are preserved during molecular growing, supporting FBDD principles.
Fragment crystallization is effective for achieving comprehensive binding pocket exploration.
Crystallization additives can offer valuable insights for structure-based drug design.