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Related Concept Videos

Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...
Factors Affecting Dissolution: Drug Permeability, Stability and Stereochemistry01:20

Factors Affecting Dissolution: Drug Permeability, Stability and Stereochemistry

Orally administered drugs primarily enter the systemic circulation via passive diffusion through the intestinal membranes. The drug's absorption is influenced by drug stability in the gastrointestinal GI tract, membrane permeability, the surface area available for absorption, luminal drug concentration, and residence time in the lumen. Drug permeability can be enhanced by adjusting the lipophilicity, polarity, or molecular size of the drug, promoting its passive transport across intestinal...
Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
Solvating Effects02:12

Solvating Effects

An understanding of the solvating effect helps rationalize the relation between solvation and acidity of the compound. In addition, this also explains the relative stability of conjugate bases for compounds with different pKa values. This lesson details, in-depth, the principle of solvating effects. The strength of an acid and the stability of its corresponding conjugate base are determined using pKa values. This observed relationship is a consequence of solvation, which is the interaction...
Entropy and Solvation02:05

Entropy and Solvation

The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ ≥ 15); an...
Factors Influencing Drug Absorption: Physicochemical Parameters01:22

Factors Influencing Drug Absorption: Physicochemical Parameters

The physicochemical characteristics of drugs play a crucial role in formulating stable and bioavailable drug products. The solubility of a drug, governed by the varying pH along the GI tract and its dissociation constant (pKa), is pivotal in determining its ionization state and absorption rate. Notably, weak acids and bases remain unionized and are absorbed more rapidly.
Enhanced drug absorption can be achieved by reducing particle sizes and increasing surface areas, thereby facilitating...

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Related Experiment Video

Updated: May 26, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Accounting for solvent in structure-based drug design.

Leslie W Tari1

  • 1Trius Therapeutics, San Diego, CA, USA. ltari@triusrx.com

Methods in Molecular Biology (Clifton, N.J.)
|January 7, 2012
PubMed
Summary

Ordered water molecules are vital for protein-ligand interactions. This chapter discusses their reliability in crystal structures and thermodynamic roles for structure-guided drug design.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Water molecules are frequently observed at protein-ligand interfaces in X-ray crystal structures.
  • These ordered waters are critical for mediating protein-ligand interactions.

Purpose of the Study:

  • To discuss the accuracy and reliability of ordered water molecules in protein-ligand crystal structures.
  • To describe the thermodynamic aspects of water's role in ligand binding.
  • To provide practical guidelines for structure-guided lead optimization concerning ordered waters.

Main Methods:

  • Review of X-ray crystallography data for protein-ligand complexes.
  • Thermodynamic analysis of water's contribution to binding energy.
  • Analysis of structure-activity relationships in lead optimization.

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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

Related Experiment Videos

Last Updated: May 26, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

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

Main Results:

  • Ordered waters are a reliable feature in high-resolution crystal structures.
  • Water molecules can significantly contribute to binding affinity through various thermodynamic interactions.
  • Understanding water's role is crucial for effective structure-based drug design.

Conclusions:

  • Ordered water molecules are integral to protein-ligand binding and should be considered in drug design.
  • Accurate assessment of water's thermodynamic contribution aids in optimizing ligand binding.
  • Guidelines for handling ordered waters can improve structure-guided lead optimization strategies.