title: Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors.
abstract: Target-specific scoring methods are more commonly used to identify small-molecule inhibitors among compounds docked to a target of interest. Top candidates that emerge from these methods have rarely been tested for activity and specificity across a family of proteins. In this study we docked a chemical library into CaMKIIδ, a member of the Ca2+/calmodulin (CaM)-dependent protein kinase (CaMK) family, and re-scored the resulting protein-compound structures using Support Vector Machine SPecific (SVMSP), a target-specific method that we developed previously. Among the 35 selected candidates, three hits were identified, such as quinazoline compound 1 (KIN-1; N4-[7-chloro-2-[(E)-styryl]quinazolin-4-yl]-N1,N1-diethylpentane-1,4-diamine), which was found to inhibit CaMKIIδ kinase activity at single-digit micromolar IC50. Activity across the kinome was assessed by profiling analogues of 1, namely 6 (KIN-236; N4-[7-chloro-2-[(E)-2-(2-chloro-4,5-dimethoxyphenyl)vinyl]quinazolin-4-yl]-N1,N1-diethylpentane-1,4-diamine), and an analogue of hit compound 2 (KIN-15; 2-[4-[(E)-[(5-bromobenzofuran-2-carbonyl)hydrazono]methyl]-2-chloro-6-methoxyphenoxy]acetic acid), namely 14 (KIN-332; N-[(E)-[4-(2-anilino-2-oxoethoxy)-3-chlorophenyl]methyleneamino]benzofuran-2-carboxamide), against 337 kinases. Interestingly, for compound 6, CaMKIIδ and homologue CaMKIIγ were among the top ten targets. Among the top 25 targets of 6, IC50values ranged from 5 to 22 μm. Compound 14 was found to be not specific toward CaMKII kinases, but it does inhibit two kinases with sub-micromolar IC50values among the top 25. Derivatives of 1 were tested against several kinases including several members of the CaMK family. These data afforded a limited structure-activity relationship study. Molecular dynamics simulations with explicit solvent followed by end-point MM-GBSA free-energy calculations revealed strong engagement of specific residues within the ATP binding pocket, and also changes in the dynamics as a result of binding. This work suggests that target-specific scoring approaches such as SVMSP may hold promise for the identification of small-molecule kinase inhibitors that exhibit some level of specificity toward the target of interest across a large number of proteins.
authors.affiliation: Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.|Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, 46202, USA.
authors.forename: David
authors.initials: D
authors.lastname: Xu
authors.affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA.
authors.forename: Liwei
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA.
authors.forename: Donghui
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA.
authors.forename: Degang
authors.initials: D
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA.|Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
authors.forename: Andy
authors.initials: A
authors.lastname: Hudmon
authors.affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Van Nuys Medical Science Building, MS 4023, 635 Barnhill Drive, Indianapolis, IN, 46202-5122, USA.|Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.|Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.|Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
authors.forename: Samy O
authors.identifier: 0000-0002-3948-7499
authors.initials: SO
authors.lastname: Meroueh
mesh_terms: D000595:Amino Acid Sequence; D054732:Calcium-Calmodulin-Dependent Protein Kinase Type 2 / Q000037:antagonists & inhibitors*; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D047428:Protein Kinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D017386:Sequence Homology, Amino Acid; D054852:Small Molecule Libraries; D013329:Structure-Activity Relationship
chemical_list: D047428:Protein Kinase Inhibitors; D054852:Small Molecule Libraries; D054732:Calcium-Calmodulin-Dependent Protein Kinase Type 2
keywords: Docking; Kinases; Molecular dynamics; Support vector machines; Target specificity