The Kinase Knowledgebase (KKB) is an Eidogen-Sertanty's database of kinase structure-activity and chemical synthesis data (register to download a free sample dataset in IJC or SDF format). The KKB represents the first gene-family wide implementation of our proprietary web-based technology for the capture, curation, and display of biological activity and chemical synthesis data from scientific literature and patent. Kinase Knowledgebase (KKB™), a small molecule activity data is manually curated by a experienced team of PhD chemists and biologists from patents and peer-reviewed publications.

The Q2 2011 release covers 7,428 journal articles and patents with 23,119 annotated assay protocols including 545,000 Biological Activity Data Points and 441 unique targets. KKB™ incorporated a number of concepts by which the data is organized including standardized HUGO gene targets where possible. For a more comprehensive list of all SAR data points for each target, please contact us.

Computational scientists will find Eidogen-Sertanty's knowledgebase to be an exceptional source for high quality training sets to build predictive QSAR models. All SAR data undergoes rigorous quality control. Every data point is associated with detailed bio assay protocols and is classified by:

• Standardized gene name
• Binding mode Assay type
• Additional in vitro data, e.g. cellular potency/cell line
• Efficacy data in appropriate animal models

We select the most relevant data such as in vitro enzyme activity data - in particular IC50 values - for the development of QSAR models (ePotency and eSelectivity), and cell-based activity and toxicity data for the development of advanced activity models (eADME and eTox).

Our curation process also captures chemical synthesis steps for those kinase inhibitors with detailed experimental procedures. Chemistry information is organized by protocols of generic reaction sequences incorporating synthetically feasible reagents that are reported in the context of the claims of a patent. This not only generates all specific examples from a patent, but also a comprehensive ensemble of structures - the patent space - that can possibly be made by the reported synthetic methodology, and which are potentially relevant within the biological activity class. Synthetic pathways leading to these molecules are structurally linked to the biological information.

Value to Drug Discovery

The knowledgebase is designed to support medicinal chemists during all project stages of drug discovery. We work closely with our clients to ensure that they receive all the relevant information around their targets and anti-targets.

At the start of a lead discovery project, the Kinase Knowledgebase provides an overview of published knowledge and patents around kinase targets of therapeutic importance, enabling a detailed understanding of the knowledge space around the target of interest and the relevant anti-targets. The presentation of inhibitor structural data makes it easy to group known inhibitors in scaffold groups and lay out a project plan around patentable chemotypes.

In the lead discovery and optimization phase of a project, the knowledgebase helps to prioritize compounds for synthesis or purchase based on their predicted properties. Based on the high quality content we have captured, we have developed nearly 50 kinase-specific eScreen® modules useful for potency and selectivity prediction, lead optimization and scaffold jumping.

Applications

• Map out patent landscape around inhibitors for kinase targets of interest.
• Organize known inhibitors into scaffold groups, including detailed synthesis steps.
• Use predicted properties and eScreen® data to prioritize compounds for synthesis or purchase.
• Utilize large quantities of descriptive SAR data to enable scaffold jumping.

Data Access

The Kinase Knowledgebase is designed such that it can be used by every scientist in the drug discovery team, even those without special training in the computational sciences.

The KKB can either be accessed online through the webPort™ platform or purchased for integration into in-house databases. Data is also available in different formats, including IJC, SD and TDT ASCII format. also offer KKB™ for QSAR and modeling. In this KKB™ version high-quality concentration response end points of biochemical assays are aggregated by unique chemical structures across assay protocols and unique HUGO kinase targets and the end points are reported as p-values. The aggregated release of KKB™ does not require any pre-processing or further standardization and can directly be used to develop QSAR or categorization models. For QSAR and modeling purposes, we also offer Pipeline Protocols that can be used as they are or as basis to create more complex protocols.

Interested in checking if a substructure exists within the Kinase Knowledgebase? Click below to build a substructure search...

To find out more about licensing terms and arrange a product demonstration, please contact us at info@eidogen-sertanty.com