A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry.
A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.
Scott
Duncan E
DE
University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
Dawes
Gwen J
GJ
Ando
Michiyo
M
Abell
Chris
C
Ciulli
Alessio
A
D000241:Adenosine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D020650:Combinatorial Chemistry Techniques / Q000379:methods*; D018360:Crystallography, X-Ray; D004220:Disulfides / Q000737:chemistry; D015195:Drug Design; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D010453:Peptide Synthases / Q000378:metabolism; D011487:Protein Conformation; D013872:Thionucleosides / Q000138:chemical synthesis / Q000737:chemistry*
D004220:Disulfides; D013872:Thionucleosides; C063476:5'-thioadenosine; D010453:Peptide Synthases; C022318:pantothenate synthetase; D000241:Adenosine