A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry

Area of Science:

• Medicinal Chemistry
• Biochemistry
• Structural Biology

Background:

• Enzymes frequently feature adenosine recognition sites, crucial for various biological processes.
• Fragment-based drug design and dynamic combinatorial chemistry (DCC) are powerful techniques for identifying enzyme inhibitors.

Purpose of the Study:

• To develop a new strategy combining fragment-based drug design and DCC for targeting adenosine-binding enzymes.
• To identify and optimize inhibitors for Mycobacterium tuberculosis pantothenate synthetase.

Main Methods:

• Utilized 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in DCC libraries.
• Employed High-Performance Liquid Chromatography (HPLC) for library analysis.
• Conducted X-ray crystallography and isothermal titration calorimetry for structural and binding studies.

Main Results:

• Identified a benzyl disulfide derivative as an initial hit.
• Optimized the hit compound to a novel meta-nitrobenzyl fragment targeting the pantoate binding site.
• Demonstrated proof-of-concept for the combined strategy.

Conclusions:

• The developed strategy is effective for probing enzyme active sites, particularly those with adenosine recognition motifs.
• This approach has broad applicability for discovering inhibitors of adenylate-forming ligases, kinases, ATPases, and other related proteins.