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Related Concept Videos

Protein-Drug Binding: Mechanism and Kinetics01:16

Protein-Drug Binding: Mechanism and Kinetics

1.8K
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,...
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Factors Affecting Protein-Drug Binding: Drug-Related Factors01:18

Factors Affecting Protein-Drug Binding: Drug-Related Factors

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Drug binding to proteins is a complex phenomenon influenced by various drug-related factors, each playing a significant role in the interaction between drugs and proteins within the body.
One crucial factor in drug-protein binding is the drug's lipophilicity or its affinity for fat. More lipophilic drugs tend to have higher binding extents. For example, highly lipophilic drugs like cloxacillin exhibit substantial protein binding, with as much as 95% of the drug binding to proteins. In...
486
Factors Affecting Protein-Drug Binding: Drug Interactions01:23

Factors Affecting Protein-Drug Binding: Drug Interactions

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Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...
605
Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

568
Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be...
568
Drug Distribution: Plasma Protein Binding01:29

Drug Distribution: Plasma Protein Binding

8.9K
Drugs predominantly attach to plasma proteins, with only a small percentage remaining unbound. The unbound portion can be calculated as one minus the bound fraction. Acidic drugs form large, inactive complexes by reversibly binding to plasma albumin, which prevents them from diffusing across biological barriers. These drug-protein complexes act as reservoirs for the drugs. As the concentration of unbound drugs decreases, these complexes quickly dissociate to release the free drug, maintaining...
8.9K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

658
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...
658

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Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms
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Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

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A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics.

Susanta Haldar1, Federico Comitani, Giorgio Saladino

  • 1Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , BS8 1TS , United Kingdom.

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|September 14, 2018
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Optimizing drug-target binding kinetics is challenging. A new method combining enhanced sampling and QM/MM simulations accurately predicts binding, revealing polarization

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Drug-target binding kinetics influences in vivo efficacy and toxicity.
  • Rational optimization of binding kinetics for improved drug potency and reduced side effects is difficult.
  • Molecular simulations face challenges with long time scales and limited force field accuracy for binding events.

Purpose of the Study:

  • To develop and test a novel computational method for accurately characterizing drug-target binding kinetics.
  • To investigate the role of electronic polarization in drug-protein interactions.
  • To provide insights into the binding mechanism of the anticancer drug Imatinib to Src kinase.

Main Methods:

  • Combined enhanced sampling simulations with quantum mechanics/molecular mechanics (QM/MM) calculations at the BLYP/VDZ level.
  • Computed association free energy profiles.
  • Characterized binding kinetics via the structure and dynamics of the transition state ensemble.

Main Results:

  • The combined approach successfully computed association free energy profiles and characterized binding kinetics.
  • Significant changes in electronic polarization were observed along the binding pathways.
  • These polarization changes were found to affect the predicted binding kinetics.

Conclusions:

  • The developed QM/MM and enhanced sampling method accurately predicts drug-target binding kinetics.
  • Electronic polarization plays a significant role in ligand-protein binding.
  • This approach has widespread importance for understanding and optimizing ligand-protein interactions.