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Related Concept Videos

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand-gated Ion Channels01:19

Ligand-gated Ion Channels

Ligand-gated ion channels are transmembrane proteins with a channel for ions to pass through and a binding site for a ligand. The channel opens only when a ligand attaches to the binding site.
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that include the...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...

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Updated: Jun 12, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

MORPH: a new tool for ligand design.

Brett R Beno1, David R Langley

  • 1Computer-Assisted Drug Design Department, Applied Biotechnology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, USA. Brett.Beno@bms.com

Journal of Chemical Information and Modeling
|May 21, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces MORPH, a software tool for modifying aromatic rings in molecules to improve drug properties. MORPH aids in creating novel drug candidates by systematically altering ring structures while maintaining key molecular features.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Aromatic ring replacement is a key strategy in drug discovery to enhance compound properties.
  • Existing methods for modifying aromatic moieties can be complex and time-consuming.

Purpose of the Study:

  • To introduce MORPH, a user-friendly software tool for systematic modification of aromatic rings in molecular models.
  • To enable the creation of novel compounds with potentially improved pharmacokinetic and pharmacodynamic profiles.

Main Methods:

  • MORPH systematically modifies aromatic rings in 3D molecular models without altering non-hydrogen atom coordinates.
  • The tool handles individual and fused ring systems.
  • MORPH includes filtering capabilities based on hydrogen-bond donors/acceptors and heteroatom count.

Main Results:

  • MORPH facilitates the exploration of diverse chemical structures through aromatic ring modifications.
  • The software allows for targeted design by filtering compounds based on specific structural criteria.
  • Application to ligands for cyclin-dependent kinase 2 (CDK2) demonstrates its utility in drug discovery.

Conclusions:

  • MORPH is an effective tool for medicinal chemists to generate novel drug candidates.
  • The software aids in optimizing molecular properties by enabling systematic aromatic ring substitution.
  • MORPH supports structure-based drug design by facilitating the modification of key molecular scaffolds.