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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
06:17

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Published on: February 28, 2025

Scaling covalent ligand discovery through dynamic combinatorial library-versus-proteome screening.

Yuchen Huang1,2, Lexuan Hou1,3, Ruiping He4

  • 1Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.

Nature Communications
|June 19, 2026
PubMed
Summary

We developed a new "library-versus-proteome" platform for faster drug discovery. This method screens many compounds simultaneously, identifying potent covalent inhibitors for various enzymes and revealing new biological roles.

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Last Updated: Jun 21, 2026

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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
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Area of Science:

  • Chemical Biology
  • Proteomics
  • Drug Discovery

Background:

  • Mass spectrometry-based chemical proteomics offers unbiased assessment of ligand interactions.
  • Current screening methods are limited by low throughput and reliance on pre-synthesized compound libraries.

Purpose of the Study:

  • To develop a high-throughput, mechanism-driven platform for real-time ligand selection and optimization.
  • To establish a "screen first, synthesize later" paradigm for efficient ligand discovery.

Main Methods:

  • Coupling dynamic combinatorial libraries with activity-based protein profiling in a "library-versus-proteome" approach.
  • Application to discover covalent inhibitors of serine hydrolases and cysteine-targeting ligands.
  • Utilizing a gel-based assay for rapid screening of compound analogues.

Main Results:

  • Increased screening throughput by 10- to 20-fold.
  • Discovered covalent inhibitors for serine hydrolases (PPME1, ABHD11, PNPLA6) and identified novel roles for PNPLA6.
  • Achieved proteome-wide EC50 profiling of over 2600 cysteines, yielding inhibitors for multiple targets including VCP.
  • Uncovered a GPCR-mediated signaling axis influencing the unfolded protein response.
  • Identified a potent VCP ligand with nanomolar activity and in vivo antitumor efficacy.

Conclusions:

  • The "library-versus-proteome" screening strategy is a scalable and efficient method for ligand discovery.
  • This platform accelerates the identification of potent ligands and provides insights into biological pathways.
  • The approach is versatile, applicable to various target classes including serine hydrolases and cysteine-containing proteins.