NMR-based techniques in the hit identification and optimisation processes

In this review, the use of general NMR spectroscopy techniques to detect ligand binding and to monitor enzyme kinetics and inhibition, which appear particularly useful in hit identification and validation, is reiterated. Furthermore, the use of NMR-based strategies for lead optimisations that are based on either iterative derivatisations of an initial core structure or on linking fragments that occupy adjacent pockets in the target’s binding site will also be described. Several recent examples will be reported and the use of these techniques in cases when the three dimensional structure of the target protein is known will be discussed.

[1]  Johan Schultz,et al.  Site-selective labeling strategies for screening by NMR. , 2002, Combinatorial chemistry & high throughput screening.

[2]  A. Hengge,et al.  The Catalytic Mechanism of Cdc25A Phosphatase* , 2002, The Journal of Biological Chemistry.

[3]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[4]  Dawoon Jung,et al.  Discovery of a novel class of reversible non-peptide caspase inhibitors via a structure-based approach. , 2005, Journal of medicinal chemistry.

[5]  Kurt Wüthrich,et al.  The second decade — into the third millenium , 1998, Nature Structural Biology.

[6]  M. Kajiwara,et al.  Screening system for urease inhibitors using 13C-NMR. , 1998, Chemical & pharmaceutical bulletin.

[7]  Maurizio Pellecchia,et al.  Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules. , 2004, Chemistry & biology.

[8]  J. Peng,et al.  Nuclear magnetic resonance-based approaches for lead generation in drug discovery. , 2001, Methods in enzymology.

[9]  Wolfgang Jahnke,et al.  Second-site NMR screening and linker design. , 2003, Current topics in medicinal chemistry.

[10]  E. Gentil,et al.  In situ 19F NMR spectroscopy study of enzymatic transglycosylation reactions using α-d-aldohexopyranosyl fluorides as donors and acceptors , 2001 .

[11]  Nicola Mongelli,et al.  Reliable high-throughput functional screening with 3-FABS. , 2004, Drug discovery today.

[12]  D. Smith,et al.  Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. , 1988, Gene.

[13]  S. Grdadolnik,et al.  Glucose transporter of Escherichia coli: NMR characterization of the phosphocysteine form of the IIB(Glc) domain and its binding interface with the IIA(Glc) subunit. , 1997, Biochemistry.

[14]  J. T. Gerig Fluorine nuclear magnetic resonance of fluorinated ligands. , 1989, Methods in enzymology.

[15]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[16]  P. Hajduk,et al.  Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. , 1999, Journal of medicinal chemistry.

[17]  Lewis C Cantley,et al.  The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor , 2004, Nature Structural &Molecular Biology.

[18]  Wolfgang Jahnke,et al.  Second-Site NMR Screening with a Spin-Labeled First Ligand , 2000 .

[19]  G. Fogliatto,et al.  WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability , 2001, Journal of biomolecular NMR.

[20]  R. London,et al.  The inter-ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands , 1999, Journal of biomolecular NMR.

[21]  P. Hajduk,et al.  A Strategy for High-Throughput Assay Development Using Leads Derived from Nuclear Magnetic Resonance-Based Screening , 2002, Journal of biomolecular screening.

[22]  Stephen W. Fesik,et al.  One-Dimensional Relaxation- and Diffusion-Edited NMR Methods for Screening Compounds That Bind to Macromolecules , 1997 .

[23]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[24]  Ajay,et al.  The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. , 1999, Chemistry & biology.

[25]  Maurizio Pellecchia,et al.  NMR-based structural characterization of large protein-ligand interactions , 2002, Journal of biomolecular NMR.

[26]  N. Shimba,et al.  NMR-based screening method for transglutaminases: rapid analysis of their substrate specificities and reaction rates. , 2002, Journal of agricultural and food chemistry.

[27]  Thomas Peters,et al.  NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. , 2003, Angewandte Chemie.

[28]  D. Sem,et al.  NMR in the acceleration of drug discovery. , 2001, Current opinion in drug discovery & development.

[29]  P. Hajduk,et al.  Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.

[30]  R. Clark,et al.  Consensus scoring for ligand/protein interactions. , 2002, Journal of molecular graphics & modelling.

[31]  Claudio Dalvit,et al.  NMR screening techniques in drug discovery and drug design , 2002 .

[32]  Lee Fielding,et al.  NMR methods for the determination of protein-ligand dissociation constants. , 2003, Current topics in medicinal chemistry.

[33]  A. Alonso,et al.  Aurintricarboxylic Acid Blocks in Vitro and in Vivo Activity of YopH, an Essential Virulent Factor of Yersinia pestis, the Agent of Plague* , 2003, Journal of Biological Chemistry.

[34]  Xiaoling Xie,et al.  Application of NMR screening in drug discovery. , 2003, Current topics in medicinal chemistry.

[35]  G. Salvesen,et al.  Caspases: preparation and characterization. , 1999, Methods.

[36]  Tudor I. Oprea,et al.  Property distribution of drug-related chemical databases* , 2000, J. Comput. Aided Mol. Des..

[37]  D. Wyss Structure-guided applications in drug discovery. , 2003, Drug discovery today.

[38]  Gang Liu,et al.  Discovery and structure-activity relationship of oxalylarylaminobenzoic acids as inhibitors of protein tyrosine phosphatase 1B. , 2003, Journal of medicinal chemistry.

[39]  G. Bemis,et al.  The properties of known drugs. 1. Molecular frameworks. , 1996, Journal of medicinal chemistry.

[40]  Maurizio Pellecchia,et al.  Selective Incorporation of 19F‐Labeled Trp Side Chains for NMR‐Spectroscopy‐Based Ligand–Protein Interaction Studies , 2003, Chembiochem : a European journal of chemical biology.

[41]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[42]  C. Venkatachalam,et al.  LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.

[43]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[44]  Bernd Meyer,et al.  Characterization of Ligand Binding by Saturation Transfer Difference NMR Spectroscopy. , 1999, Angewandte Chemie.

[45]  Maurizio Pellecchia,et al.  Use of selective Trp side chain labeling to characterize protein-protein and protein-ligand interactions by NMR spectroscopy. , 2003, Journal of the American Chemical Society.

[46]  Stefan Knapp,et al.  High-throughput NMR-based screening with competition binding experiments. , 2002, Journal of the American Chemical Society.

[47]  Jeffrey W. Peng,et al.  Applications of SHAPES screening in drug discovery. , 2002, Combinatorial chemistry & high throughput screening.

[48]  W. Jahnke,et al.  Protein NMR in biomedical research , 2004, Cellular and Molecular Life Sciences CMLS.

[49]  P. Hajduk,et al.  Integration of NMR and high-throughput screening. , 2002, Combinatorial chemistry & high throughput screening.

[50]  Nicola Mongelli,et al.  A general NMR method for rapid, efficient, and reliable biochemical screening. , 2003, Journal of the American Chemical Society.

[51]  J C Reed,et al.  IAP family proteins--suppressors of apoptosis. , 1999, Genes & development.

[52]  Marina Veronesi,et al.  Competition binding experiments for rapidly ranking lead molecules for their binding affinity to human serum albumin. , 2002, Combinatorial chemistry & high throughput screening.

[53]  P. Hajduk,et al.  NMR-based screening in drug discovery , 1999, Quarterly Reviews of Biophysics.

[54]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[55]  Thomas Lengauer,et al.  Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.

[56]  M. Sundström,et al.  Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water* , 2000, Journal of biomolecular NMR.

[57]  Kurt Wüthrich,et al.  Nmr in drug discovery , 2002, Nature Reviews Drug Discovery.

[58]  Thomas Lengauer,et al.  A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.

[59]  Marina Veronesi,et al.  Fluorine-NMR competition binding experiments for high-throughput screening of large compound mixtures. , 2002, Combinatorial chemistry & high throughput screening.

[60]  D. Gorenstein Phosphorus-31 nuclear magnetic resonance of enzyme complexes: bound ligand structure, dynamics, and environment. , 1989, Methods in enzymology.