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Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design.

ABSTRACT: Cyclin-dependent kinases (CDKs) belong to the CMGC subfamily of protein kinases and play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been reported to be implicated in the cell cycle regulation in vertebrates. These CDKs are highly homologous and contain a conserved catalytic core. This makes the design of inhibitors specific for a particular CDK difficult. There is, however, growing need for CDK5 specific inhibitors to treat various neurodegenerative diseases. Recently, cis-substituted cyclobutyl-4-aminoimidazole inhibitors have been identified as potent CDK5 inhibitors that gave up to 30-fold selectivity over CDK2. Available IC50 values also indicate a higher potency of this class of inhibitors over commercially available drugs, such as roscovitine. To understand the molecular basis of higher potency and selectivity of these inhibitors, here, we present molecular dynamics simulation results of CDK5/p25 and CDK2/CyclinE complexed with a series of cyclobutyl-substituted imidazole inhibitors and roscovitine. The atomic details of the stereospecificity and selectivity of these inhibitors are obtained from energetics and binding characteristics to the CDK binding pocket. The study not only complements the experimental findings, but also provides a wealth of detailed information that could help the structure-based drug designing processes.

SUBMITTER: Rath SL

PROVIDER: S-EPMC3772847 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design.

Rath Soumya Lipsa SL Senapati Sanjib S

PloS one 20130913 9

Cyclin-dependent kinases (CDKs) belong to the CMGC subfamily of protein kinases and play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been reported to be implicated in the cell cycle regulation in vertebrates. These CDKs are highly homologous and contain a conserved catalytic core. This makes the design of inhibitors specific for a particular CDK difficult. There is, however, growing need for CDK5 specific inhibitors to treat various neurodegenerative disea ...[more]

PMID: 24058495

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Project description:Chromatographic characterization and parameterization studies targeting many solutes require the judicious choice of operating conditions to minimize analysis time without compromising the accuracy of the results. To minimize analysis time, solutes are often grouped into a small number of mixtures; however, this increases the risk of peak overlap. While multivariate curve resolution methods are often able to resolve analyte signals based on their spectral qualities, these methods require that the chromatographically overlapped compounds have dissimilar spectra. In this work, a strategy for grouping compounds into sample mixtures containing solutes with distinct spectral and, optionally, with distinct chromatographic properties, in order to ensure successful solute resolution either chromatographically or with curve resolution methods is proposed. We name this strategy rational design of mixtures (RDM). RDM utilizes multivariate selectivity as a metric for making decisions regarding group membership (i.e., whether to add a particular solute to a particular sample). A group of 97 solutes was used to demonstrate this strategy. Utilizing both estimated chromatographic properties and measured spectra to group these 97 analytes, only 12 groups were required to avoid a situation where two or more solutes in the same group could not be resolved either chromatographically (i.e., they have significantly different retention times) or spectrally (i.e., spectra are different enough to enable resolution by curve resolution methods). When only spectral properties were utilized (i.e., the chromatographic properties are unknown ahead of time) the number of groups required to avoid unresolvable overlaps increased to 20. The grouping strategy developed here will improve the time and instrument efficiency of studies that aim to obtain retention data for solutes as a function of operating conditions, whether for method development or determination of the chromatographic parameters of solutes of interest (e.g., k w ).

Dataset Information

Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design.

Publications

Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design.

Similar Datasets

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