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Related Concept Videos

Protein-Drug Binding: Mechanism and Kinetics01:16

Protein-Drug Binding: Mechanism and Kinetics

1.7K
Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
1.7K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

616
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
616
Protein Networks02:26

Protein Networks

4.5K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

14.9K
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:
14.9K
Nonlinear Pharmacokinetics: Bioavailability and Protein-Drug Binding01:22

Nonlinear Pharmacokinetics: Bioavailability and Protein-Drug Binding

589
When a drug follows nonlinear pharmacokinetics, its bioavailability, the amount of the drug that reaches the systemic circulation, can change with different doses. This is due to the presence of a saturable pathway. The pathway becomes saturated as the drug concentration increases, decreasing the absorption rate. Consequently, the drug's bioavailability may be lower than expected at higher doses.
To quantify the extent of bioavailability, pharmacologists often use a parameter called .
589

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Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects
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COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale.

Hanfeng Lin1,2,3, Bin Yang1,2, Lang Ding3,4

  • 1The Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.

Nature Communications
|September 30, 2025
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Summary

COOKIE-Pro is a new proteomics method to measure how covalent inhibitors bind to proteins. This tool helps optimize drug potency and selectivity for better covalent therapeutics development.

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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
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Area of Science:

  • Biochemistry
  • Chemical Biology
  • Proteomics

Background:

  • Covalent inhibitors are a promising therapeutic class.
  • Existing methods for profiling covalent inhibitor binding kinetics and selectivity are limited.
  • Comprehensive proteome-wide analysis is needed to understand off-target effects.

Purpose of the Study:

  • Introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), a novel method for quantifying covalent inhibitor binding kinetics.
  • Enable unbiased, proteome-wide assessment of inhibitor interactions.
  • Facilitate optimization of covalent drug potency and selectivity.

Main Methods:

  • Utilizes a two-step incubation process combined with mass spectrometry-based proteomics.
  • Determines kinact and KI values for covalent inhibitors.
  • Applies a streamlined two-point strategy for high-throughput screening.

Main Results:

  • COOKIE-Pro accurately quantifies covalent inhibitor binding kinetics on a proteome-wide scale.
  • Validated using BTK inhibitors, reproducing known parameters and identifying off-targets.
  • Revealed spebrutinib is more potent against TEC kinase than BTK.
  • Generated thousands of kinetic profiles from covalent fragment screening.

Conclusions:

  • COOKIE-Pro is a powerful tool for preclinical covalent drug development.
  • Enables quantitative decoupling of reactivity and affinity at scale.
  • Provides a comprehensive view of covalent inhibitor binding, aiding in optimizing drug properties.