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Updated: Feb 25, 2026

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
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Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Published on: April 17, 2017

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KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange

Jia Lu1, Rane A Harrison2, Lianbo Li1

  • 1Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.

Structure (London, England : 1993)
|August 8, 2017
PubMed

Insights

Researchers used HDX-MS to study KRAS G12C conformations targeted by SIIP binders. A new SIIP configuration was found with a quinazoline inhibitor, aiding structure-guided drug design for non-small-cell lung cancer.

Area of Science:

  • Oncology
  • Structural Biology
  • Biochemistry

Background:

  • KRAS G12C is a common mutation in non-small-cell lung cancer (NSCLC).
  • Targeting KRAS involves inhibiting its guanine nucleotide pocket or an inducible pocket (SIIP) near switch motifs.
  • SIIP binders may interact with diverse KRAS conformations due to switch II flexibility.

Purpose of the Study:

  • To differentiate KRAS switch II conformations induced by distinct SIIP binder chemical classes.
  • To elucidate the structural basis for observed HDX-MS differences.
  • To identify novel SIIP configurations relevant for drug design.

Main Methods:

  • Hydrogen/deuterium-exchange mass spectrometry (HDX MS) to analyze protein backbone dynamics.
  • X-ray crystallography to determine high-resolution protein structures.
  • Utilizing two chemical classes of SIIP binders to probe KRAS conformations.

Main Results:

  • HDX MS successfully discriminated between KRAS switch II conformations induced by different SIIP binders.
  • X-ray crystallography revealed the structural basis for HDX MS findings.
  • A novel SIIP configuration was identified upon binding of a quinazoline-based inhibitor.

Conclusions:

  • HDX MS is effective for characterizing KRAS conformational states induced by SIIP binders.
  • The discovery of a new SIIP configuration offers insights for structure-guided drug design.
  • These findings advance the development of targeted therapies for KRAS-mutated NSCLC.
Keywords:
RAScovalent inhibitordrug discoveryprotein dynamics

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