BoBER: web interface to the base of bioisosterically exchangeable replacements.

Area of Science:

• Medicinal Chemistry
• Computational Drug Design
• Bioinformatics

Background:

• Bioisosterism and scaffold hopping are crucial strategies in drug discovery for optimizing compound properties.
• Existing methods for identifying bioisosteric replacements can be time-consuming and limited in scope.
• There is a need for accessible tools to facilitate the exploration of chemical space in drug design.

Purpose of the Study:

• To introduce the Base of Bioisosterically Exchangeable Replacements (BoBER) web server.
• To provide a user-friendly platform for searching bioisosteric and scaffold hopping replacements.
• To aid medicinal chemists in generating novel ideas for drug optimization.

Main Methods:

• Developed a freely available web server, BoBER.
• Created a database of bioisosteric and scaffold hopping replacements by mining the Protein Data Bank.
• Implemented an interface for fast and user-friendly searches.

Main Results:

• The BoBER web server provides a comprehensive database of potential replacements.
• Demonstrated the utility of BoBER using an existing MurF inhibitor as an example.
• The server enables rapid identification of novel replacement strategies.

Conclusions:

• BoBER is a valuable resource for medicinal chemists.
• The web server facilitates the discovery of improved drug candidates through bioisosteric and scaffold hopping.
• BoBER can accelerate the hit-to-lead optimization process in drug design.