Discovery of Small Molecules that Inhibit the Disordered Protein, p27(Kip1).
Disordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27(Kip1) (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).
Department of Structural Biology, Memphis, TN 38105.|Department of Developmental Neurobiology, Memphis, TN 38105.
Luigi I
LI
Iconaru
Department of Structural Biology, Memphis, TN 38105.
David
D
Ban
Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105.
Kavitha
K
Bharatham
Computational Science and Engineering Division, Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830.
Arvind
A
Ramanathan
Department of Structural Biology, Memphis, TN 38105.
Weixing
W
Zhang
Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105.
Anang A
AA
Shelat
Department of Developmental Neurobiology, Memphis, TN 38105.
Jian
J
Zuo
Department of Structural Biology, Memphis, TN 38105.|Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163.
Richard W
RW
Kriwacki
D051357:Cyclin-Dependent Kinase 2 / Q000378:metabolism; D050760:Cyclin-Dependent Kinase Inhibitor p27 / Q000378:metabolism*; D016213:Cyclins / Q000378:metabolism; D006801:Humans; D011485:Protein Binding / Q000187:drug effects; D060066:Protein Interaction Maps / Q000187:drug effects; D054852:Small Molecule Libraries / Q000494:pharmacology*; D013329:Structure-Activity Relationship
D016213:Cyclins; D054852:Small Molecule Libraries; D050760:Cyclin-Dependent Kinase Inhibitor p27; C495894:CDK2 protein, human; D051357:Cyclin-Dependent Kinase 2