Chapter 11
Fragment Screening by NMR
Ben J. Davis
Abstract
This chapter describes the use of NMR to screen a fragment library as part of a fragment-based lead
discovery (FBLD) campaign. The emphasis is on the practicalities involved in fragment screening by NMR,
with particular attention to the use of 1D ligand-observed
1 H NMR experiments. An overview of the
theoretical considerations underlying the choice of method and experimental configuration is given, along
with a discussion of steps that can be taken in order to minimize the risk of experimental artifacts often
associated with the identification of low-affinity interactions.
Key words NMR, Fragment screening, Drug discovery, FBLD , Fragment-based lead discovery,
Biophysics
1 Introduction
Since its inception in the early 2000s, fragment-based lead discovery (FBLD) has become a widely used method for hit identification
in early-stage drug discovery [1–6]. “Fragment-based lead discovery” refers to the identification of low-molecular-weight molecules,
which bind to the macromolecular target of interest, and the
subsequent evolution of these molecules into classical highly potent
ligands and drugs [7–11]. Several marketed drugs have been developed using FBLD methods [12, 13], and at least 40 more compounds are currently in clinical trials [14], demonstrating the
widespread applicability and utility of the approach.
The essential premise of FBLD is to use a robust assay to screen
a library of fragments and thus to identify which of those fragments
interact with a defined molecular target (Fig. 1). The key feature of
FBLD is that the initially screened fragments are smaller, and
therefore tend to be of lower affinity, than is the case for most
other hit identification methods. The initial screen must be able
to identify these weak interactions, and this imposes a number of
constraints on the assay used: it must be sensitive, often being
required to work with a K D in the high μM or low mM range; the
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5_11, © Springer Science+Business Media, LLC, part of Springer Nature 2021
247
Fragment Screening by NMR
Ben J. Davis
Abstract
This chapter describes the use of NMR to screen a fragment library as part of a fragment-based lead
discovery (FBLD) campaign. The emphasis is on the practicalities involved in fragment screening by NMR,
with particular attention to the use of 1D ligand-observed
1 H NMR experiments. An overview of the
theoretical considerations underlying the choice of method and experimental configuration is given, along
with a discussion of steps that can be taken in order to minimize the risk of experimental artifacts often
associated with the identification of low-affinity interactions.
Key words NMR, Fragment screening, Drug discovery, FBLD , Fragment-based lead discovery,
Biophysics
1 Introduction
Since its inception in the early 2000s, fragment-based lead discovery (FBLD) has become a widely used method for hit identification
in early-stage drug discovery [1–6]. “Fragment-based lead discovery” refers to the identification of low-molecular-weight molecules,
which bind to the macromolecular target of interest, and the
subsequent evolution of these molecules into classical highly potent
ligands and drugs [7–11]. Several marketed drugs have been developed using FBLD methods [12, 13], and at least 40 more compounds are currently in clinical trials [14], demonstrating the
widespread applicability and utility of the approach.
The essential premise of FBLD is to use a robust assay to screen
a library of fragments and thus to identify which of those fragments
interact with a defined molecular target (Fig. 1). The key feature of
FBLD is that the initially screened fragments are smaller, and
therefore tend to be of lower affinity, than is the case for most
other hit identification methods. The initial screen must be able
to identify these weak interactions, and this imposes a number of
constraints on the assay used: it must be sensitive, often being
required to work with a K D in the high μM or low mM range; the
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5_11, © Springer Science+Business Media, LLC, part of Springer Nature 2021
247