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Related Concept Videos

Targets for Drug Action: Overview01:26

Targets for Drug Action: Overview

Drugs target macromolecules to modify ongoing cellular processes. Primary drug targets include receptors, ion channels, transporters, and enzymes.
Receptors are either membrane-spanning or intracellular proteins, which upon binding a ligand, get activated and transmit the signal downstream to elicit a response. Drugs bind receptors, either mimicking the action of endogenous ligands or blocking the receptor activity to bring about a modified response. Nearly 35% of approved drugs target the G...
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.
In...
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...
Principles of Drug Action01:24

Principles of Drug Action

Drugs are chemical substances that modify biological responses by interacting with macromolecular targets such as receptors, ion channels, transporters, and enzymes. Pharmacodynamics describes the course of action of drugs leading to the physiological effect at a specific site in the body.
Drugs can be agonists or antagonists. Like the endogenous ligands, agonists always bind and activate the target to produce a cellular response. Agonist binding induces a conformational change which in turn...
Drug-Receptor Interactions01:29

Drug-Receptor Interactions

Drug-receptor interaction describes the binding of receptors by drugs, but not all drug-receptor interactions result in activation and tissue response. For instance, the binding of agonists activates the receptor to generate a cellular reaction, while antagonists bind to receptors without causing their activation.
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue.

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Related Experiment Video

Updated: Jun 2, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

How does a drug molecule find its target binding site?

Yibing Shan1, Eric T Kim, Michael P Eastwood

  • 1D. E. Shaw Research, New York, New York 10036, USA.

Journal of the American Chemical Society
|May 7, 2011
PubMed
Summary

Molecular dynamics simulations captured drug molecules like dasatinib binding to protein targets, revealing the atomic-level process. This method aids in discovering new drug binding sites, especially for allosteric inhibitors.

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Protein Target Prediction and Validation of Small Molecule Compound

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Pharmacology

Background:

  • Understanding drug-target interactions is crucial for drug development.
  • Experimental characterization of drug binding pathways remains challenging.
  • Thermodynamic principles of molecular binding are established but lack dynamic detail.

Purpose of the Study:

  • To simulate and visualize the complete atomic-level process of drug-protein binding.
  • To investigate the role of intermediate conformations and water molecules in binding.
  • To develop a novel simulation technique for identifying drug binding sites, including allosteric ones.

Main Methods:

  • Unguided, long molecular dynamics simulations were performed.
  • Ligands (dasatinib, PP1) were placed randomly near the target protein (Src kinase).
  • Simulations tracked the entire binding process from initial contact to complex formation.

Main Results:

  • Simulations successfully reproduced crystallographically determined drug-protein complexes.
  • Continuous, atomic-level trajectories revealed intermediate binding conformations.
  • The role of water molecules in the binding pathway was elucidated.

Conclusions:

  • The unguided simulation method effectively captures drug-protein binding events.
  • This technique provides unprecedented insight into dynamic binding processes.
  • The approach is valuable for discovering novel allosteric binding sites and developing new inhibitors.