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Related Concept Videos

Drug Discovery: Overview01:26

Drug Discovery: Overview

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Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
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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.
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The receptor occupancy theory connects a drug's response to the number of occupied receptors. With higher drug concentrations, more receptors are occupied, leading to increased responses. The formation of drug-receptor complexes involves association and dissociation rates, which reach equilibrium when the forward and backward reactions are equal. The equilibrium association constant (Ka) and its inverse, the equilibrium dissociation constant (Kd), indicate drug affinity. Higher Ka and lower...
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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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Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
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Dynamic Docking: A Paradigm Shift in Computational Drug Discovery.

Dario Gioia1, Martina Bertazzo2,3, Maurizio Recanatini4

  • 1Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy. dario.gioia2@unibo.it.

Molecules (Basel, Switzerland)
|November 23, 2017
PubMed
Summary
This summary is machine-generated.

Dynamic docking using molecular dynamics (MD) offers a more comprehensive approach to in silico drug discovery than traditional static methods. This advanced technique promises to revolutionize lead candidate identification by exploring binding mechanisms and kinetics more accurately.

Keywords:
binding kineticsdrug discoveryenhanced samplingmolecular dynamicsprotein-ligand binding

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Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Molecular Modeling

Background:

  • Traditional molecular docking methods have limitations due to static or semi-flexible treatments of protein-ligand interactions.
  • These methods often neglect crucial factors like solvation and entropic effects, reducing their predictive accuracy.
  • The need for more robust in silico methods is critical for efficient drug discovery.

Purpose of the Study:

  • To review the advancements in molecular dynamics (MD) based 'dynamic docking' as an alternative to traditional docking.
  • To highlight the progress enabling full exploration of drug-target recognition and binding mechanisms.
  • To discuss the potential of dynamic docking to replace static approaches in drug discovery.

Main Methods:

  • Utilizing full atomistic molecular dynamics (MD) simulations for macromolecular complexes.
  • Exploring mechanistic and energetic aspects of drug-target recognition and binding.
  • Determining binding and unbinding kinetic constants.

Main Results:

  • MD-based dynamic docking provides a more comprehensive understanding of protein-ligand interactions compared to static methods.
  • Advancements in computing power and simulation methodologies are making dynamic docking more feasible.
  • This approach allows for detailed mechanistic and energetic insights into binding events.

Conclusions:

  • Dynamic docking, powered by MD, represents a significant advancement over traditional docking techniques.
  • It offers superior mechanistic and energetic insights into drug-target interactions.
  • Dynamic docking is poised to become the standard for in silico drug discovery, marking a paradigm shift.