Structural bioinformatics-based design of selective, irreversible kinase inhibitors

Area of Science:

• Biochemistry
• Structural Biology
• Pharmacology

Background:

• Protein kinase active sites are highly conserved across 491 human domains.
• Designing selective inhibitors for protein kinases presents a significant challenge.

Purpose of the Study:

• To identify structural features conferring selectivity for p90 ribosomal protein S6 kinase (RSK).
• To design and validate a selective inhibitor targeting RSK.

Main Methods:

• Utilized a structural bioinformatics approach to analyze protein kinase active sites.
• Designed a fluoromethylketone inhibitor targeting identified RSK selectivity filters (threonine and cysteine).
• Tested inhibitor potency and selectivity in mammalian cells, including genetically modified kinases.

Main Results:

• Identified a threonine and a cysteine as key selectivity filters in the RSK active site.
• Developed a fluoromethylketone inhibitor that potently and selectively inactivated RSK1 and RSK2.
• Demonstrated that kinases lacking one or both filters were resistant, but became sensitive upon filter introduction.

Conclusions:

• Two specific amino acids (threonine and cysteine) are sufficient to confer inhibitor sensitivity to RSK.
• This finding provides a basis for developing highly selective kinase inhibitors.