Computational methods for scaffold hopping

  • What are the advantages of scaffold hopping?

    Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties..

  • What are the classification of scaffold hopping?

    In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping..

  • What are the different methods of scaffold hopping?

    Scaffold hopping is the identification of isofunctional molecular structures with chemically completely different core structures.
    It is a subset of bioisosteric replacement where the core motif (pharmacophore) is replaced.
    Important interaction potentials of the molecule are usually maintained..

  • What is an example of scaffold hopping?

    The transformation from morphine to tramadol by ring opening is one of the earliest examples of scaffold hopping [4]..

  • What is lead hopping in drug discovery?

    In lead hopping, the goal is to identify compounds that retain the desirable biological activity of the original lead compound while avoiding its limitations, such as toxicity or poor pharmacokinetic properties..

  • What is scaffold hopping?

    Scaffold hopping, also known as lead hopping [5,6], is one strategy for discovering structurally novel compounds [7].
    Scaffold hopping methods typically start with known active compounds and end with a novel chemotype by modifying the central core structure of the molecule [3]..

  • Core hopping allows for the rapid screening of novel cores to help overcome unwanted properties by generating new lead compounds with improved core properties while preserving key R-group interactions.
  • Scaffold matrices can be used to achieve drug delivery with high loading and efficiency to specific sites.
    Biomaterials used for fabrication of scaffold may be natural polymers such as alginate, proteins, collagens, gelatin, fibrins, and albumin, or synthetic polymers such as polyvinyl alcohol and polyglycolide.
  • Scaffold: A term describing the core structure of a compound or series.
    Substitution site: Position (site) of chemical variation in a core structure carrying different substituents (functional groups, R-groups) in different analogs.
2.
  • 2.1. Scaffold hopping based on pharmacophore.
  • 2.2. Based on the search for similarity.
  • 2.3. Scaffold hopping based on fragment replacement.
  • 2.4. Scaffold hopping based on machine learning.
  • 2.5. Scaffold hopping based on biological activity similarity.
The computational method for scaffold hopping which is based on biological activity similarity avoids using compound structural descriptors and attempts to overcome the limitations of traditional methods for scaffold hopping.
We reviewed the computational methods for scaffold hopping and divided them into five categories: pharmacophore based, similarity based, fragment replacement based, machine learning based and biological activity similarity based.

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