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Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays
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Knowledge-based scoring functions in drug design. 1. Developing a target-specific method for kinase-ligand

Mengzhu Xue1, Mingyue Zheng, Bing Xiong

  • 1State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai, China 201203.

Journal of Chemical Information and Modeling
|August 5, 2010
PubMed
Summary

A new scoring function, kinase-PMF, enhances drug discovery by specifically assessing ATP-competitive kinase inhibitor binding. This target-specific approach improves prediction power in structure-based drug design compared to general methods.

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Published on: October 26, 2015

Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Pharmacology

Background:

  • Protein kinases are crucial therapeutic targets in numerous diseases.
  • Developing effective ATP-competitive kinase inhibitors is vital for drug discovery.
  • Existing scoring functions may lack specificity for kinase targets.

Purpose of the Study:

  • To develop and evaluate a kinase family-specific potential of mean force (PMF) scoring function, termed kinase-PMF.
  • To assess the performance of kinase-PMF in predicting the binding of ATP-competitive kinase inhibitors.
  • To demonstrate the advantage of target-specific scoring functions over general ones in structure-based drug design.

Main Methods:

  • Derived kinase-PMF potentials using a dataset of 872 kinase complexes.
  • Inherited functions and atom types from the established PMF04 scoring function.
  • Evaluated kinase-PMF performance on an external test set of 128 kinase crystal structures.
  • Compared kinase-PMF against eight common scoring functions using retrieval rates and virtual screening.

Main Results:

  • Kinase-PMF demonstrated improved performance in assessing kinase inhibitor binding.
  • The target-specific scoring function outperformed general scoring functions in prediction power.
  • Evaluation included retrieval of correct conformations and virtual screening efficacy.

Conclusions:

  • Target-specific scoring functions, like kinase-PMF, offer a promising strategy to enhance prediction accuracy in structure-based drug design.
  • Kinase-PMF provides a valuable tool for researchers in the field of kinase inhibitor development.
  • A publicly accessible web service for kinase-PMF rescoring is available.