Fragment-based drug discovery applied to Hsp90. Discovery of two lead series with high ligand efficiency.

Inhibitors of the chaperone Hsp90 are potentially useful as chemotherapeutic agents in cancer. This paper describes an application of fragment screening to Hsp90 using a combination of NMR and high throughput X-ray crystallography. The screening identified an aminopyrimidine with affinity in the high micromolar range and subsequent structure-based design allowed its optimization into a low nanomolar series with good ligand efficiency. A phenolic chemotype was also identified in fragment screening and was found to bind with affinity close to 1 mM. This fragment was optimized using structure based design into a resorcinol lead which has subnanomolar affinity for Hsp90, excellent cell potency, and good ligand efficiency. This fragment to lead campaign improved affinity for Hsp90 by over 1,000,000-fold with the addition of only six heavy atoms. The companion paper (DOI: 10.1021/jm100060b) describes how the resorcinol lead was optimized into a compound that is now in clinical trials for the treatment of cancer.

[1]  S. Lindquist,et al.  HSP90 and the chaperoning of cancer , 2005, Nature Reviews Cancer.

[2]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[3]  X. Barril,et al.  Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms. , 2004, Chemistry & biology.

[4]  Christopher W Murray,et al.  Fragment-based lead discovery using X-ray crystallography. , 2005, Journal of medicinal chemistry.

[5]  Y. Janin.  Heat Shock Protein 90 Inhibitors. A Text Book Example of Medicinal Chemistry , 2006 .

[6]  G. V. Paolini,et al.  Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..

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

[8]  Jonathan Weissman,et al.  Molecular Chaperones and Protein Quality Control , 2006, Cell.

[9]  L. Pearl,et al.  NVP-AUY922: a novel heat shock protein 90 inhibitor active against xenograft tumor growth, angiogenesis, and metastasis. , 2008, Cancer research.

[10]  L. Pearl,et al.  Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin. , 1999, Journal of medicinal chemistry.

[11]  Sreenath V. Sharma,et al.  Development of radicicol analogues. , 2003, Current cancer drug targets.

[12]  P. Leeson,et al.  The influence of drug-like concepts on decision-making in medicinal chemistry , 2007, Nature Reviews Drug Discovery.

[13]  Gurmeet Kaur,et al.  Antiangiogenic Properties of 17-(Dimethylaminoethylamino)-17-Demethoxygeldanamycin , 2004, Clinical Cancer Research.

[14]  J. Lyons,et al.  Biological characterization of AT7519, a small-molecule inhibitor of cyclin-dependent kinases, in human tumor cell lines , 2009, Molecular Cancer Therapeutics.

[15]  L. Pearl,et al.  Structure and mechanism of the Hsp90 molecular chaperone machinery. , 2006, Annual review of biochemistry.

[16]  R. Nilakantan,et al.  Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90. , 2008, Journal of medicinal chemistry.

[17]  Marcel L Verdonk,et al.  Automated Protein–Ligand Crystallography for Structure‐Based Drug Design , 2006, ChemMedChem.

[18]  Michèle N Schulz,et al.  Recent progress in fragment-based lead discovery. , 2009, Current opinion in pharmacology.

[19]  Giulio Rastelli,et al.  Structure‐Based and in silico Design of Hsp90 Inhibitors , 2009, ChemMedChem.

[20]  R. Glen,et al.  Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.

[21]  A. Hopkins,et al.  Ligand efficiency: a useful metric for lead selection. , 2004, Drug discovery today.

[22]  K. Gajiwala,et al.  Dihydroxyphenylisoindoline amides as orally bioavailable inhibitors of the heat shock protein 90 (hsp90) molecular chaperone. , 2010, Journal of medicinal chemistry.

[23]  Paul Workman,et al.  The identification, synthesis, protein crystal structure and in vitro biochemical evaluation of a new 3,4-diarylpyrazole class of Hsp90 inhibitors. , 2005, Bioorganic & medicinal chemistry letters.

[24]  L. Fritz,et al.  A high-affinity conformation of Hsp90 confers tumour selectivity on Hsp90 inhibitors , 2003, Nature.

[25]  Mark Whittaker,et al.  Fragment‐based Identification of Hsp90 Inhibitors , 2009, ChemMedChem.

[26]  D. Solit,et al.  Development and application of Hsp90 inhibitors. , 2008, Drug discovery today.

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

[28]  F. Allen.  The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[29]  P. Workman.  Combinatorial attack on multistep oncogenesis by inhibiting the Hsp90 molecular chaperone. , 2004, Cancer letters.

[30]  B. Sigurskjold,et al.  Exact analysis of competition ligand binding by displacement isothermal titration calorimetry. , 2000, Analytical biochemistry.

[31]  M. Adler,et al.  Potent Triazolothione Inhibitor of Heat‐Shock Protein‐90 , 2009, Chemical biology & drug design.

[32]  B. Blagg,et al.  Hsp90 inhibitors: Small molecules that transform the Hsp90 protein folding machinery into a catalyst for protein degradation , 2006, Medicinal research reviews.

[33]  Andrew R Leach,et al.  Fragment screening: an introduction. , 2006, Molecular bioSystems.

[34]  Jean M. Severin,et al.  Discovery and Design of Novel HSP90 Inhibitors Using Multiple Fragment‐based Design Strategies , 2007, Chemical biology & drug design.

[35]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[36]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[37]  James R. Porter,et al.  Design, synthesis, and biological evaluation of hydroquinone derivatives of 17-amino-17-demethoxygeldanamycin as potent, water-soluble inhibitors of Hsp90. , 2006, Journal of medicinal chemistry.

[38]  Xavier Barril,et al.  Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design. , 2005, Journal of medicinal chemistry.

[39]  E Blanc,et al.  Electronic Reprint Biological Crystallography Modelling Prior Distributions of Atoms for Macromolecular Refinement and Completion Roversi Et Al. ¯ Prior Distributions for Macromolecular Refinement and Completion , 2022 .

[40]  N. Rosen,et al.  Targeting wide-range oncogenic transformation via PU24FCl, a specific inhibitor of tumor Hsp90. , 2004, Chemistry & biology.

[41]  D. Fattori,et al.  Molecular recognition: the fragment approach in lead generation. , 2004, Drug discovery today.

[42]  Roman A. Laskowski,et al.  PDBsum: summaries and analyses of PDB structures , 2001, Nucleic Acids Res..

[43]  Michael J. Hartshorn,et al.  AstexViewerTM †: a visualisation aid for structure-based drug design , 2002, J. Comput. Aided Mol. Des..

[44]  L. Neckers,et al.  The benzoquinone ansamycin 17-allylamino-17-demethoxygeldanamycin binds to HSP90 and shares important biologic activities with geldanamycin , 1998, Cancer Chemotherapy and Pharmacology.

[45]  Laura G. Dubois,et al.  Discovery of novel 2-aminobenzamide inhibitors of heat shock protein 90 as potent, selective and orally active antitumor agents. , 2009, Journal of Medicinal Chemistry.

[46]  S. Jackson,et al.  Mechanistic studies on Hsp90 inhibition by ansamycin derivatives. , 2007, Journal of molecular biology.

[47]  Xiong Cai,et al.  Cancer Therapy : Preclinical CUDC-305 , a Novel Synthetic HSP 90 Inhibitor with Unique Pharmacologic Properties for Cancer Therapy , 2009 .

[48]  B. Blagg,et al.  Hsp90 Inhibitors: Small Molecules that Transform the Hsp90 Protein Folding Machinery into a Catalyst for Protein Degradation. , 2006 .

[49]  Paul Workman,et al.  Drugging the Cancer Chaperone HSP90 , 2007, Annals of the New York Academy of Sciences.

[50]  Richard D. Taylor,et al.  Modeling water molecules in protein-ligand docking using GOLD. , 2005, Journal of medicinal chemistry.

[51]  R. Korsmeyer,et al.  Simple stereoselective synthesis of (.+-.)-oplopanone , 1978 .

[52]  M. Drysdale,et al.  Medicinal chemistry of Hsp90 inhibitors. , 2008, Current topics in medicinal chemistry.

[53]  Gianni Chessari,et al.  From fragment to clinical candidate--a historical perspective. , 2009, Drug discovery today.

[54]  W Bruce Turnbull,et al.  On the value of c: can low affinity systems be studied by isothermal titration calorimetry? , 2003, Journal of the American Chemical Society.

[55]  Neal Rosen,et al.  Crystal Structure of an Hsp90–Geldanamycin Complex: Targeting of a Protein Chaperone by an Antitumor Agent , 1997, Cell.

[56]  A DOUBLE BLIND COMPARISON OF DOXAPRAM, ETHAMIVAN AND METHYLPHENIDATE. , 1965 .

[57]  P. Leeson,et al.  A comparison of physiochemical property profiles of development and marketed oral drugs. , 2003, Journal of medicinal chemistry.

[58]  Mike Wood,et al.  4,5-diarylisoxazole Hsp90 chaperone inhibitors: potential therapeutic agents for the treatment of cancer. , 2007, Journal of medicinal chemistry.

[59]  D. Erlanson.  Fragment-based lead discovery: a chemical update. , 2006, Current opinion in biotechnology.

[60]  Marcel L Verdonk,et al.  Group Efficiency: A Guideline for Hits‐to‐Leads Chemistry , 2008, ChemMedChem.

[61]  Richard D. Taylor,et al.  Improved protein–ligand docking using GOLD , 2003, Proteins.

[62]  Paul Watson,et al.  A web-based platform for virtual screening. , 2003, Journal of molecular graphics & modelling.

[63]  Daniel A. Erlanson,et al.  Fragment‐Based Drug Discovery. , 2004 .

[64]  F. Hartl,et al.  In Vivo Function of Hsp90 Is Dependent on ATP Binding and ATP Hydrolysis , 1998, The Journal of cell biology.

[65]  X. Barril,et al.  Combining hit identification strategies: fragment-based and in silico approaches to orally active 2-aminothieno[2,3-d]pyrimidine inhibitors of the Hsp90 molecular chaperone. , 2009, Journal of medicinal chemistry.

[66]  L. Neckers,et al.  Tumor selectivity of Hsp90 inhibitors: the explanation remains elusive. , 2006, ACS chemical biology.

[67]  Martin Head-Gordon,et al.  Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package , 2006 .

[68]  L. Neckers,et al.  Geldanamycin as a Potential Anti-Cancer Agent: Its Molecular Target and Biochemical Activity , 2004, Investigational New Drugs.

[69]  M. Congreve,et al.  Recent developments in fragment-based drug discovery. , 2008, Journal of medicinal chemistry.

[70]  Andrew R. Leach,et al.  Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery , 2001, J. Chem. Inf. Comput. Sci..

[71]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[72]  Michael J Hartshorn,et al.  AstexViewer: a visualisation aid for structure-based drug design. , 2002, Journal of computer-aided molecular design.

[73]  P. Hajduk,et al.  A decade of fragment-based drug design: strategic advances and lessons learned , 2007, Nature Reviews Drug Discovery.

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

[75]  J. Lyons,et al.  Biological characterization of AT 7519 , a small-molecule inhibitor of cyclin-dependent kinases , in human tumor cell lines , 2009 .

[76]  Alexander A Alex,et al.  Fragment-based drug discovery: what has it achieved so far? , 2007, Current topics in medicinal chemistry.

[77]  5-Aryl-4-(5-substituted-2,4-dihydroxyphenyl)-1,2,3-thiadiazoles as inhibitors of Hsp90 chaperone. , 2009, Bioorganic & medicinal chemistry letters.

[78]  Ian A. Watson,et al.  Characteristic physical properties and structural fragments of marketed oral drugs. , 2004, Journal of medicinal chemistry.

[79]  I. Kuntz,et al.  The maximal affinity of ligands. , 1999, Proceedings of the National Academy of Sciences of the United States of America.