SLAS Discovery - Special Issue on Advances in MALDI Mass Spectrometry for Drug Discovery - Volume 22 Issue 10 - December 2017 - 1211

712761
research-article2017

JBXXXX10.1177/2472555217712761Slas Discovery: Advancing Life Sciences R&DVanderPorten et al.

Original Research

Identification of Small-Molecule Noncovalent
Binders Utilizing SAMDI Technology

SLAS Discovery
2017, Vol. 22(10) 1211-1217
© 2017 Society for Laboratory
Automation and Screening
https://doi.org/10.1177/2472555217712761
DOI: 10.1177/2472555217712761
journals.sagepub.com/home/jbx

Erica C. VanderPorten1, Michael D. Scholle2, John Sherrill2,
John C. Tran1, and Yichin Liu1

Abstract
In recent years, the ability to unambiguously identify complex mixtures of analytes with high accuracy and resolving power
in a label-free format continues to expand the application of mass spectrometry (MS) in the drug discovery process. This
advantage combined with improved instrumentation makes MS suitable for targets with limited alternative assays for
high-throughput screening (HTS). We describe a novel screening format using Self-Assembled Monolayers and matrixassisted laser Desorption Ionization (SAMDI) technology. SAMDI enables affinity capture of a target protein for use in a
small-molecule-binding assay format. Subsequent ionization enables the inferred identification of noncovalent compound
interactions. SAMDI technology overcomes shot-to-shot variability by uniformly saturating the surface with captured
protein, thereby minimizing matrix crystallization "hot spots." Furthermore, the combination with high-resolution matrixassisted laser desorption/ionization time of flight significantly reduces interference of small-molecule detection from salt,
detergent, and matrix. By using a pooled library format, the SAMDI assay can significantly improve the throughput of
MS-based screening irrespective of enzyme activity. Finally, we demonstrate binding affinity rank ordering from a pool of
compounds that correlates with potency data from a biochemical assay.
Keywords
MALDI, SAMDI, noncovalent binder, mass spectrometry

Introduction
The drug discovery process executes conventional compound
library screenings using fluorescence- and chemiluminescencebased detection that affords screening throughput of more than
100,000 compounds per day. However, these detection readouts are prone to interference with compound libraries and can
lead to high false-positive rates. The process of confirming real
hits and eliminating false-positives can require a number of
dose-response triage assays that demand additional time,
reagents, and human resources.
Mass spectrometry (MS) can unambiguously identify complex mixtures of analytes with high accuracy and resolving
power in a label-free detection format. This advantage makes
MS suitable for screening small-molecule compound libraries
as new target classes emerge with increasing complexity and
limited availability of labeled detection reagents. Limitations
on the existing MS front-end technology, however, constrains
the sampling rate and throughput despite the fact that modern
mass spectrometers can scan as rapidly as tens of microseconds. For electrospray, Agilent RapidFire MS1 remains stateof-the-art technology, allowing medium throughput in
384-well format and has been implemented as high-throughput
screening (HTS) triage where samples can be analyzed in as
fast as 15 s. However, this throughput is insufficient for

screening libraries that can well surpass 1 million compounds.
For reference, a RapidFire MS point screen covers <5% of a
typical small-molecule compound library in the same amount
of time that a fluorescent-based assay can be executed.
As an alternative to electrospray,2 matrix-assisted laser
desorption/ionization (MALDI)3 is amenable to speeds
required for ultra-high-throughput screening (i.e., >100,000
samples per day).4-8 While MALDI can be more tolerable to
salt and detergent, sample cleanup is critical to ensure a highquality MS response.9 While cleanup has historically been
achieved through solid phase extraction, affinity capture has
been previously used in conjunction with MALDI.10,11 The
SAMDI technology12,13 pioneered by the Mrksich lab, enables
1

Biochemical and Cellular Pharmacology Department, Genentech Inc.,
San Francisco, CA, USA
2
SAMDI Tech, Inc., Chicago, IL, USA
Received Apr 1, 2017, and in revised form Apr 28, 2017, Accepted for
publication May 10, 2017.
Supplementary material is available online with this article.
Corresponding Author:
Yichin Liu, Biochemical and Cellular Pharmacology Department,
Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
Email: liu.yichin@gene.com

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