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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 11, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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SENSAAS-Bioisostere: A computational method for 3D shape-guided bioisosteric replacements and scaffold-hopping.

Louis Somme1, Yassin Es Saim2, Frédéric Payan2

  • 1Université Côte d'Azur, Inserm U1323, CNRS UMR7275, IPMC, 660 route des lucioles 06560, Valbonne, France.

European Journal of Medicinal Chemistry
|June 9, 2026
PubMed
Summary

SENSAAS-Bioisostere is a new computational method for drug discovery. It identifies bioisosteric replacements and performs scaffold-hopping by comparing molecular fragments based on shape and pharmacophore similarity.

Keywords:
3D point clouds3D shapeBioisosteric replacementCheminformaticsFragmentsMolecular similarityScaffold-hoppingShape-based similarity

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Identifying novel drug candidates often involves exploring bioisosteric replacements and scaffold-hopping.
  • Existing methods may lack the precision to effectively compare molecular fragments for similarity.

Purpose of the Study:

  • To introduce SENSAAS-Bioisostere, a computational method for identifying bioisosteric replacements and scaffold-hopping.
  • To enable the design of new molecules with similar shapes and pharmacophores to existing drug fragments.

Main Methods:

  • Utilizes the SENSAAS method's matching and sub-matching properties to compare molecular fragments.
  • Represents fragments as colored 3D point clouds capturing shape, pharmacophore, and substituent information.
  • Employs 3D point set registration for aligning molecular fragments by minimizing point distances.

Main Results:

  • SENSAAS-Bioisostere successfully identifies fragments with similar shape and pharmacophore properties.
  • The method builds and aligns new molecules based on query fragments.
  • Retrospective analysis confirmed the effectiveness of the approach in scaffold-hopping for new molecule discovery.

Conclusions:

  • SENSAAS-Bioisostere is an effective computational tool for bioisosteric replacement and scaffold-hopping.
  • The method facilitates the search for novel drug candidates by leveraging fragment similarity.
  • The unique representation and alignment approach enhance the accuracy of molecular comparison.