The small-molecule inhibitor selectivity between IKKα and IKKβ kinases in NF-κB signaling pathway.
The enzyme complex IκB kinase (IKK) is an essential activator of NF-κB signaling pathway involved in propagating the cellular response to inflammation. The complex contains two functional subunits IKKα and IKKβ, which are structurally conserved kinases and selective inhibition of them would result in distinct biological effects. However, most existing IKK inhibitors show moderate or high promiscuity for the two homologous kinases. Understanding of the molecular mechanism and biological implication underlying the specific interactions in IKK-ligand recognition is thus fundamentally important for the rational design of selective IKK inhibitors. In the current work, we integrated molecular docking, quantum mechanics/molecular mechanics calculation and Poisson-Boltzmann/surface area analysis to investigate the structural basis and energetic property of the selective binding of small-molecule ligands to IKKα and IKKβ. It was found that the selectivity is primarily determined by the size and topology difference in ATP-binding pocket of IKKα and IKKβ kinase domains; bulky inhibitor molecules commonly have, respectively, low and appropriate affinities towards IKKα and IKKβ, and thus exhibit relatively high selectivity for IKKβ over IKKα, whereas small ligands can only bind weakly to both the two kinases with low selectivity. In addition, the conformation, arrangement and distribution of residues in IKK pockets are also responsible for constituting the exquisite specificity of ligand binding to KKα and IKKβ. Next, a novel quantitative structure-selectivity relationship model was developed to characterize the relative contribution of each kinase residue to inhibitor selectivity and to predict the selectivity and specificity for a number of known IKK inhibitors. Results showed that the active-site residues contribute significantly to the selectivity by directly interacting with inhibitor ligands, while those protein portions far away from the kinase active sites may also play an important role in determining the selectivity through long-range non-bonded forces and indirect allosteric effect.
a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .|b School of Life Science and Engineering , Southwest Jiaotong University , Chengdu , China , and.
Feifei
F
Tian
c Center of Bioinformatics (COBI), School of Life Science and Technology , University of Electronic Science and Technology of China (UESTC) , Chengdu , China.
Peng
P
Zhou
b School of Life Science and Engineering , Southwest Jiaotong University , Chengdu , China , and.
Wenyuan
W
Kang
a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .
Li
L
Luo
a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .
Xia
X
Fan
a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .
Jun
J
Yan
a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .
Huaping
H
Liang
D000595:Amino Acid Sequence; D020134:Catalytic Domain; D006801:Humans; D051550:I-kappa B Kinase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000378:metabolism*; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D017434:Protein Structure, Tertiary; D021281:Quantitative Structure-Activity Relationship; D011789:Quantum Theory; D015398:Signal Transduction / Q000187:drug effects; D040681:Structural Homology, Protein
D016328:NF-kappa B; D047428:Protein Kinase Inhibitors; C496559:CHUK protein, human; D051550:I-kappa B Kinase; C496560:IKBKB protein, human
IKKα/IKKβ; NF-κB; inflammation; ligand selectivity; small-molecule inhibitor