Design and synthesis of novel lactate dehydrogenase A inhibitors by fragment-based lead generation.

Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using fragment-based lead generation (FBLG), assisted by X-ray crystallography to develop small molecule LDHA inhibitors. Fragment hits were identified through NMR and SPR screening and optimized into lead compounds with nanomolar binding affinities via fragment linking. Also reported is their modification into cellular active compounds suitable for target validation work.

[1]  Daniel R. Caffrey,et al.  Structure-based maximal affinity model predicts small-molecule druggability , 2007, Nature Biotechnology.

[2]  M. Threadgill,et al.  Poly(ADP-ribose)polymerase inhibition - where now? , 2005, Current medicinal chemistry.

[3]  K. Sreekumar,et al.  First Example of Organocatalysis by Polystyrene-Supported PAMAM Dendrimers: Highly Efficient and Reusable Catalyst for Knoevenagel Condensations , 2008 .

[4]  J. Pflugrath,et al.  The finer things in X-ray diffraction data collection. , 1999, Acta crystallographica. Section D, Biological crystallography.

[5]  A. Giatromanolaki,et al.  Lactate dehydrogenase-5 (LDH-5) overexpression in non-small-cell lung cancer tissues is linked to tumour hypoxia, angiogenic factor production and poor prognosis , 2003, British Journal of Cancer.

[6]  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.

[7]  A. Gill,et al.  New lead generation strategies for protein kinase inhibitors - fragment based screening approaches. , 2004, Mini reviews in medicinal chemistry.

[8]  Brett A Tounge,et al.  Ligand efficiency and fragment-based drug discovery. , 2009, Drug discovery today.

[9]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[10]  Niklas Blomberg,et al.  Design of compound libraries for fragment screening , 2009, J. Comput. Aided Mol. Des..

[11]  Maurizio Pellecchia,et al.  Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox. , 2004, Chemistry & biology.

[12]  J L Sussman,et al.  Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. , 1989, Journal of molecular biology.

[13]  L. Bonnac,et al.  Nicotinamide adenine dinucleotide based therapeutics. , 2008, Current medicinal chemistry.

[14]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

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

[16]  E. Giovannetti,et al.  Discovery of N-hydroxyindole-based inhibitors of human lactate dehydrogenase isoform A (LDH-A) as starvation agents against cancer cells. , 2011, Journal of medicinal chemistry.

[17]  V. Schramm,et al.  A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT , 2009, Proceedings of the National Academy of Sciences.

[18]  H. Muirhead,et al.  Design and synthesis of new enzymes based on the lactate dehydrogenase framework. , 1991, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[19]  O. Warburg [Origin of cancer cells]. , 1956, Oncologia.

[20]  L. Nicholson,et al.  Protein dynamics measurements by TROSY-based NMR experiments. , 2000, Journal of magnetic resonance.

[21]  V. J. Winter,et al.  Structural basis for altered activity of M‐ and H‐isozyme forms of human lactate dehydrogenase , 2001 .

[22]  C. Tse,et al.  ABT-263: a potent and orally bioavailable Bcl-2 family inhibitor. , 2008, Cancer research.

[23]  Chi V Dang,et al.  Cancer's molecular sweet tooth and the Warburg effect. , 2006, Cancer research.

[24]  B. R. Baker,et al.  Potential anticancer agents--L. Non-classical antimetabolites. II. Some factors in the design of exoalkylating enzyme inhibitors, particulary of lactic dehydrogenase. , 1960, Journal of medicinal and pharmaceutical chemistry.

[25]  A. Harris,et al.  Lactate dehydrogenase 5 expression in operable colorectal cancer: strong association with survival and activated vascular endothelial growth factor pathway--a report of the Tumour Angiogenesis Research Group. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[26]  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.

[27]  A. Harris,et al.  Lactate Dehydrogenase 5 Expression in Squamous Cell Head and Neck Cancer Relates to Prognosis following Radical or Postoperative Radiotherapy , 2009, Oncology.

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

[29]  Mark Whittaker,et al.  Discovery of a Novel Hsp90 Inhibitor by Fragment Linking , 2010, ChemMedChem.

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

[31]  Lance G. Laing,et al.  Advantages and application of label-free detection assays in drug screening , 2008, Expert opinion on drug discovery.

[32]  Martin Hammarström,et al.  Crystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888. , 2010, Biochemistry.

[33]  M. Waterman,et al.  Comparative biosequence metrics , 2005, Journal of Molecular Evolution.

[34]  Chris Abell,et al.  Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase. , 2009, Angewandte Chemie.

[35]  Mark Whittaker,et al.  Compound Design by Fragment‐Linking , 2011, Molecular informatics.

[36]  S. Carloni,et al.  Clean synthesis in water. Part 2: Uncatalysed condensation reaction of Meldrum's acid and aldehydes , 2001 .

[37]  K. Beaumont,et al.  Design of ester prodrugs to enhance oral absorption of poorly permeable compounds: challenges to the discovery scientist. , 2003, Current drug metabolism.

[38]  Robin Taylor,et al.  New software for searching the Cambridge Structural Database and visualizing crystal structures. , 2002, Acta crystallographica. Section B, Structural science.

[39]  K. Sugihara,et al.  Lactate Dehydrogenase-5 (LDH-5) Expression in Human Gastric Cancer: Association with Hypoxia-Inducible Factor (HIF-1α) Pathway, Angiogenic Factors Production and Poor Prognosis , 2008, Annals of Surgical Oncology.

[40]  J. Thornton,et al.  AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR , 1996, Journal of biomolecular NMR.

[41]  N. Blomberg,et al.  An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drug discovery programmes. , 2007, Current topics in medicinal chemistry.

[42]  R. Scolyer,et al.  Lactate dehydrogenase 5 expression in melanoma increases with disease progression and is associated with expression of Bcl-XL and Mcl-1, but not Bcl-2 proteins , 2010, Modern Pathology.

[43]  Araceli,et al.  Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity* , 2004, Journal of Biological Chemistry.

[44]  Gianni Chessari,et al.  Discovery of (2,4-dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-yl]methanone (AT13387), a novel inhibitor of the molecular chaperone Hsp90 by fragment based drug design. , 2010, Journal of medicinal chemistry.

[45]  G. Semenza,et al.  Inhibition of lactate dehydrogenase A induces oxidative stress and inhibits tumor progression , 2010, Proceedings of the National Academy of Sciences.

[46]  Don Liu,et al.  An Innovative Way to Create Assay Ready Plates for Concentration Response Testing using Acoustic Technology , 2010 .

[47]  M. Zloh,et al.  Targeting glycolysis: a fragment based approach towards bifunctional inhibitors of hLDH-5. , 2011, Chemical communications.

[48]  Ursula Bilitewski,et al.  Protein-sensing assay formats and devices. , 2006, Analytica chimica acta.

[49]  S J Wodak,et al.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. , 1999, Acta crystallographica. Section D, Biological crystallography.

[50]  S. Wodak,et al.  Deviations from standard atomic volumes as a quality measure for protein crystal structures. , 1996, Journal of molecular biology.

[51]  Rutger H A Folmer,et al.  Fragment screening to predict druggability (ligandability) and lead discovery success. , 2011, Drug discovery today.

[52]  D. Fattori,et al.  Fragment-Based Approach to Drug Lead Discovery , 2008, Drugs in R&D.

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

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

[55]  A. Clarke,et al.  Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. , 1999, Journal of molecular biology.

[56]  W N Hunter,et al.  Structure of trypanothione reductase from Crithidia fasciculata at 2.6 A resolution; enzyme-NADP interactions at 2.8 A resolution. , 1994, Acta crystallographica. Section D, Biological crystallography.

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

[58]  Andreas Bender,et al.  "Virtual fragment linking": an approach to identify potent binders from low affinity fragment hits. , 2008, Journal of medicinal chemistry.

[59]  J. Tolan,et al.  MDCK (Madin-Darby canine kidney) cells: A tool for membrane permeability screening. , 1999, Journal of pharmaceutical sciences.

[60]  A. Bujacz,et al.  Modeling of isotope effects on binding oxamate to lactic dehydrogenase. , 2009, The journal of physical chemistry. B.

[61]  Masaya Orita,et al.  Lead generation and examples opinion regarding how to follow up hits. , 2011, Methods in enzymology.

[62]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[63]  J. Holbrook,et al.  A general method for relieving substrate inhibition in lactate dehydrogenases. , 1999, Protein engineering.

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

[65]  Clemens Vonrhein,et al.  Data processing and analysis with the autoPROC toolbox , 2011, Acta crystallographica. Section D, Biological crystallography.