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  • Review Article
  • Published:

Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes

Nature Reviews Drug Discovery volume 5, pages 585–595 (2006)Cite this article

Key Points

  • Electrospray ionization mass spectrometry (ESI-MS) is an emerging technology for studying noncovalent ligand–macromolecular target interactions. Characterization of these interactions could provide new insights into undesirable binding interactions at earlier stages in the drug discovery process, enabling termination of the development of such compounds at an earlier stage and at less overall expense.

  • Mass spectrometry has several potential advantages over other methods used to study noncovalent complexes. Ligands or targets do not have to be labelled for detection of the complex, smaller quantities of material are required for analysis, and this technology is rapid and automatable. All these features make mass spectrometry well suited for high-throughput applications in the drug discovery process.

  • ESI-MS can be used to study ligand interactions in protein, multiprotein, DNA and RNA systems, and can provide information about binding specificity, binding affinity, binding stoichiometry, dissociation constants and gas-phase stability of ligand–target complexes. The key information generated by ESI-MS can contribute to, or drive, primary compound screening activities and structure–activity relationship (SAR) optimization.

  • ESI-MS can be used to measure the gas-phase stabilities of protein–ligand complexes, which can then be compared with solution-phase stabilities. Typically, electrostatic and H-bond contacts of inhibitors are modified during the drug development phase, and so the ability to measure the strength of these interactions by gas-phase stability measurements is useful. In the gas phase, electrostatic and H-bond interactions are favoured over hydrophobic interactions, and data interpretation must take this bias into consideration.

  • Multitarget affinity/specificity screening (MASS) enables the discovery of small-molecule ligands that bind to structured regions of RNA. In a single assay, MASS analysis can determine the chemical composition of ligands that bind to an RNA target, the relative/absolute dissociation constants, and the specificity of binding to one RNA target relative to other RNA targets.

  • MASS can also be implemented in a ligand-based lead discovery strategy in the optimization of SARs. Screening of a panel of small molecules consisting of various chemical motifs against a target using MASS identifies structural motifs that bind the target at different locations. The information generated on motif-binding sites and orientation on the target can then be used to design a single structure with higher affinity for the target.

  • Nanospray ionization uses a smaller-diameter ESI emitter (typically 2–20 ÎĽm) and offers several potential advantages over aspects of ESI-MS-based drug discovery. Significantly less sample is consumed in an analysis, with meaningful measurements being made from total sample volumes in the 1–3 ÎĽl range. Moreover, nanospray ionization is thought to be a gentler method of ionization than ESI in a conventional format, and in some cases has been shown to provide greater sensitivity than ESI (based on both less sample consumption and more efficient ion desolvation).

Abstract

For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand–macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.

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Figure 1: Potential applications of ESI-MS in drug discovery.
Figure 2: Application of ESI-FTICR mass spectrometry in ligand screening.
Figure 3: Application of ESI-MS in determining binding modes.
Figure 4: Use of DOLCE-MS to determine binding characteristics of a compound.
Figure 5: Application of MASS in the identification of small-molecule ligands that bind to structured regions of RNA.
Figure 6: Mass spectra of RNase A complexed with 2′-CMP and CTP.

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  1. A Division of ISIS Pharmaceuticals, Ibis Therapeutics, 1891 Rutherford Road, Carlsbad, 92008, California, USA

    Steven A. Hofstadler & Kristin A. Sannes-Lowery

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Glossary

Ion mobility spectrometry

The separation of ions according to their velocity through a buffer gas under the influence of an electric field.

Collisionally activated dissociation

(CAD). Dissociation is caused by collisions between ions and gaseous molecules that result in the conversion of translational energy into internal vibrational energy of the ion.

SH2 domain

(Src homology 2 domain). A protein motif that recognizes and binds tyrosine-phosphorylated sequences, and therefore has a key role in relaying cascades of signal transduction.

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Hofstadler, S., Sannes-Lowery, K. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 5, 585–595 (2006). https://doi.org/10.1038/nrd2083

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  • DOI: https://doi.org/10.1038/nrd2083

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