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Related Concept Videos

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:
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

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...
Drug-Receptor Bonds01:25

Drug-Receptor Bonds

Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
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Updated: May 13, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Using molecular docking-based binding energy to predict toxicity of binary mixture with different binding sites.

Zhifeng Yao1, Zhifen Lin, Ting Wang

  • 1State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.

Chemosphere
|March 15, 2013
PubMed
Summary
This summary is machine-generated.

Predicting chemical mixture toxicity is complex due to varied binding sites. This study proposes a general model using molecular docking-based binding energy (Ebinding) to predict toxicity in microorganisms.

Keywords:
AHsBinary mixturesBinding sitesCGsDhfrDhpsLucMolecular docking energySATMPTUTZsToxicity modelUEaldehydescyanogenicdihydrofolate synthasedihydropteroate reductaseluciferasesulfonamidetoxicity unittriazinestrimethoprimurea

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Area of Science:

  • Environmental Chemistry
  • Toxicology
  • Computational Chemistry

Background:

  • Environmental chemical pollution presents complex mixtures.
  • Individual chemicals can bind to various sites on target proteins, complicating toxicity prediction.
  • Understanding these interactions is crucial for environmental risk assessment.

Purpose of the Study:

  • To develop a general approach for predicting the toxicity of chemical mixtures.
  • To utilize molecular docking-based binding energy (Ebinding) for toxicity prediction.
  • To establish a relationship between mixture toxicity and individual chemical properties.

Main Methods:

  • Selected examples of chemical mixtures with same and different binding sites/target proteins (aldehydes, cyanogenic toxicants, triazines, urea herbicides, sulfonamides, trimethoprim).
  • Employed molecular docking to determine binding energy (Ebinding) for individual chemicals.
  • Correlated Ebinding and logKow(mix) with binary mixture toxicity (EC50M).

Main Results:

  • A general relationship was found between binary mixture toxicity (EC50M) and the binding energy (Ebinding) and logKow(mix) of individual chemicals.
  • Ebinding effectively describes how individual chemicals interact at different binding sites.
  • The proposed approach shows promise for predicting mixture toxicity.

Conclusions:

  • A general and simplified model for predicting chemical mixture toxicity to microorganisms was developed.
  • Molecular docking-based binding energy (Ebinding) is a valuable parameter for assessing mixture toxicity.
  • This approach can help understand and predict the environmental impact of complex chemical mixtures.