Contents
NMR-based Screening
Guest Editor: Philip Hajduk
Applications
of SHAPES Screening in Drug Discovery Pp.583-590
Christopher A. Lepre, Jeffrey Peng, Jasna Fejzo, Norzehan Abdul-Manan, Jennifer Pocas, Marc Jacobs, Xiaoling Xie and Jonathan M. Moore
NMR
and In silico Screening Pp.591-603
Simon
Rüdisser and Wolfgang Jahnke
Fluorine-NMR
Competition Binding Experiments for High- Throughput Screening of Large
Compound Mixtures Pp.605-611
Claudio
Dalvit, Maria Flocco, Marina Veronesi and Brian J. Stockman
Integration
of NMR and High-Throughput Screening Pp.613-621
Philip
J. Hajduk and David J. Burns
Site-Selective
Labeling Strategies for Screening by NMR Pp.623-630
Johan
Weigelt, Mats Wikström, Johan Schultz and Maria J. P. van Dongen
Utility
of NMR in Lead Optimization: Fragment-Based Approaches Pp.631-643
Jeffrey
R. Huth and Chaohong Sun
Competition
Binding Experiments for Rapidly Ranking Lead Molecules for their Binding
Affinity to Human Serum Albumin Pp.645-650
Claudio
Dalvit, Maria Flocco, Brian J. Stockman and Marina Veronesi
In
Vivo Toxicity Screening Programs Using Metabonomics Pp.651-662
Lora
C. Robosky, Donald G. Robertson, J. David Baker, Sarika Rane and Michael D.
Reily
Abstracts
[Back to top] Applications of SHAPES Screening in Drug Discovery
Christopher
A. Lepre, Jeffrey Peng, Jasna Fejzo, Norzehan Abdul-Manan, Jennifer Pocas, Marc
Jacobs, Xiaoling Xie and Jonathan M. Moore
The SHAPES strategy combines nuclear magnetic resonance (NMR) screening of a library of small drug-like molecules with a variety of complementary methods, such as virtual screening, high throughput enzymatic assays, combinatorial chemistry, X-ray crystallography, and molecular modeling, in a directed search for new medicinal chemistry leads. In the past few years, the SHAPES strategy has found widespread utility in pharmaceutical research. To illustrate a variety of different implementations of the method, we will focus in this review on recent applications of the SHAPES strategy in several drug discovery programs at Vertex Pharmaceuticals.
[Back to top] NMR
and In silico Screening
Simon
Rüdisser and Wolfgang Jahnke
NMR-based screening and virtual, or in silico, screening can be highly complementary and synergistic. NMR-based screening is a rapid and reliable method for validating hits that come from in silico screens. In addition, ligand-binding data derived from NMR-based screens can focus and direct subsequent in silico screening. We will first give a short overview of existing NMR and in silico screening methods, discuss the drawbacks associated with each, and finally present applications that highlight the combination of the two technologies.
[Back to top] Fluorine-NMR Competition Binding Experiments for High-
Throughput Screening of Large Compound Mixtures
Claudio
Dalvit, Maria Flocco, Marina Veronesi and Brian J. Stockman
High-throughput ligand-based NMR screening with competition binding experiments is extended to 19F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the 19F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the 19F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented.
[Back
to top] Integration
of NMR and High-Throughput Screening
Philip J. Hajduk and David J. Burns
NMR-based screening has become a
powerful method for the identification and analysis of lowmolecular weight
organic compounds that bind to protein targets and can be utilized in drug
discovery programs. In particular, heteronuclear NMR-based screening can yield
information about both the affinity and binding location of potential lead
compounds. In addition, heteronuclear NMR-based screening has wide applications
in complementing and facilitating conventional high-throughout screening
programs. This article will describe several strategies for the integration of
NMR-based screening and high-throughput screening. The marriage of these two
techniques promises to be of tremendous benefit in the triage of hits that come
from HTS, and can aid the medicinal chemist in the identification of quality
leads that have high potential for further optimization.
[Back
to top] Site-Selective Labeling Strategies for
Screening by NMR
Johan Weigelt, Mats Wikström, Johan Schultz and Maria J. P. van Dongen
NMR based screening has become an important tool in the pharmaceutical industry. Methods that provide information on the location of small molecule binding sites on the surface of a drug target (e. g. SAR-by-NMR and related techniques) are of particular interest. In order to extend the applicability of such techniques to drug targets of higher molecular weight, selective labeling strategies may be employed. Dual-amino acid selective labeling and site directed non-native amino acid replacement (SNAAR) allow for the selective detection of NMR resonances of a specific amino acid residue. This results in significantly reduced spectral complexity, which not only enables application to higher molecular weight systems, but also eliminates the need for sequential resonance assignment in order to identify the binding site. Regio-selective (or segmental) labeling of an entire protein domain of a multi domain protein may also be achieved. Labeling only a selected part of a multi domain protein (e. g. a catalytic or ligand binding domain) is an attractive way to simplify the spectral interpretation without disturbing the system under study.
[Back
to top] Utility of NMR in Lead Optimization: Fragment-Based
Approaches
Jeffrey R. Huth and Chaohong Sun
NMR has proven to be a valuable tool for identifying small molecule drug leads that serve as starting points for lead optimization programs. In addition, NMR screening can also be applied during lead optimization in order to improve the pharmacokinetic properties of a compound. In this paper we review the NMR methods that can be used for this purpose. Several examples are then summarized to demonstrate the usefulness of fragment-based approaches in optimizing the physical properties of potential drug candidates.
[Back
to top] Competition Binding Experiments for Rapidly
Ranking Lead Molecules for their Binding Affinity to Human Serum Albumin
Claudio Dalvit, Maria Flocco, Brian J. Stockman and Marina Veronesi
Many lead molecules that have high affinity for a therapeutic target in vitro exhibit a reduced efficacy in vivo. Drug binding to human serum albumin is a major contributor to this reduction in potency, and many drug discovery programs expend significant resources preparing compounds that have decreased albumin binding. As rational and structure-based approaches have already been demonstrated to design compounds that have reduced affinity for albumin, the ability to rapidly and accurately assess protein binding will be valuable in lead optimization. This review will summarize some of the NMR-based efforts towards developing universal, rapid, accurate, and site-specific assays for estimating protein binding.
[Back to top] In Vivo Toxicity Screening Programs Using
Metabonomics
Lora
C. Robosky, Donald G. Robertson, J. David Baker, Sarika Rane and Michael D.
Reily
Metabonomics is an emerging technology that enables rapid in vivo screening for toxicity, disease state, or drug efficacy. The technology combines the power of high-resolution nuclear magnetic resonance (NMR) techniques with statistical data analysis methods to rapidly evaluate the metabolic "status" of an animal. Complimentary to other profiling technologies like proteomics and genomics, metabonomics provides a fingerprint of the small-molecules contained in a given biofluid through the time course of a study. This article reviews the steps in implementing a metabonomics-based screening program from study design through data analysis. While metabonomics is still a relatively new technology in comparison to the other “omics”, published results from metabonomics studies demonstrate its potential impact in the drug discovery process by enabling the incorporation of safety endpoints much earlier in the drug discovery process, reducing the likelihood (and cost) of later stage attrition.