Probing the S2' Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates.

The lethal factor (LF) enzyme secreted by Bacillus anthracis is a zinc hydrolase that is chiefly responsible for anthrax-related cell death. Although many studies of the design of small molecule LF inhibitors have been conducted, no LF inhibitor is yet available as a therapeutic agent. Inhibitors with considerable chemical diversity have been developed and investigated; however, the LF S2' subsite has not yet been systematically explored as a potential target for lead optimization. Here we present synthesis, experimental evaluation, modeling, and structural biology for a novel series of sulfonamide hydroxamate LF inhibitor analogues specifically designed to extend into, and probe chemical preferences of, this S2' subsite. We discovered that this region accommodates a wide variety of chemical functionalities and that a broad selection of ligand structural modifications directed to this area can be incorporated without significant deleterious alterations in biological activity. We also identified key residues in this subsite that can potentially be targeted to improve inhibitor binding.

[1]  Elizabeth A. Amin,et al.  Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding. , 2014, Acta crystallographica. Section D, Biological crystallography.

[2]  M. Fiscella,et al.  Bacillus anthracis Protective Antigen Kinetics in Inhalation Spore-Challenged Untreated or Levofloxacin/Raxibacumab-Treated New Zealand White Rabbits , 2013, Toxins.

[3]  Elizabeth A. Amin,et al.  Development of a Comprehensive, Validated Pharmacophore Hypothesis for Anthrax Toxin Lethal Factor (LF) Inhibitors Using Genetic Algorithms, Pareto Scoring, and Structural Biology , 2012, J. Chem. Inf. Model..

[4]  M. Gaestel,et al.  Anthrax lethal toxin disrupts the endothelial permeability barrier through blocking p38 signaling , 2012, Journal of cellular physiology.

[5]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[6]  B. Sankaran,et al.  Antidotes to anthrax lethal factor intoxication. Part 3: Evaluation of core structures and further modifications to the C2-side chain. , 2012, Bioorganic & medicinal chemistry letters.

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

[8]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[9]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[10]  S. Ullrich,et al.  Raxibacumab for the treatment of inhalational anthrax. , 2009, The New England journal of medicine.

[11]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[12]  Elizabeth A. Amin,et al.  Identification of Novel Non-Hydroxamate Anthrax Toxin Lethal Factor Inhibitors by Topomeric Searching, Docking and Scoring, and in Vitro Screening , 2009, J. Chem. Inf. Model..

[13]  Etienne Weiss,et al.  Therapeutic antibodies: successes, limitations and hopes for the future , 2009, British journal of pharmacology.

[14]  C. Hansch,et al.  Combating the threat of anthrax: a quantitative structure-activity relationship approach. , 2008, Molecular pharmaceutics.

[15]  Georgios A. Dalkas,et al.  Low molecular weight inhibitors of the protease anthrax lethal factor. , 2008, Mini-Reviews in Medical Chemistry.

[16]  A. Strongin,et al.  Rhodanine Derivatives as Selective Protease Inhibitors Against Bacterial Toxins , 2008, Chemical biology & drug design.

[17]  B. Turk.  Discovery and development of anthrax lethal factor metalloproteinase inhibitors. , 2008, Current Pharmaceutical Biotechnology.

[18]  B. D. Gaddis,et al.  Inhibitors of anthrax lethal factor. , 2007, Bioorganic & medicinal chemistry letters.

[19]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[20]  Ajay N. Jain.  Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search , 2007, J. Comput. Aided Mol. Des..

[21]  M. Pellecchia,et al.  A high-throughput screening approach to anthrax lethal factor inhibition. , 2006, Bioorganic chemistry.

[22]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.

[23]  A. Khlebnikov,et al.  Novel small-molecule inhibitors of anthrax lethal factor identified by high-throughput screening. , 2006, Journal of medicinal chemistry.

[24]  T. Humphreys,et al.  Cationic polyamines inhibit anthrax lethal factor protease , 2006, BMC pharmacology.

[25]  P. Carter.  Potent antibody therapeutics by design , 2006, Nature Reviews Immunology.

[26]  E. Scolnick,et al.  The discovery of a potent and selective lethal factor inhibitor for adjunct therapy of anthrax infection. , 2006, Bioorganic & Medicinal Chemistry Letters.

[27]  A. Strongin,et al.  Anthrax lethal factor protease inhibitors: synthesis, SAR, and structure-based 3D QSAR studies. , 2006, Journal of medicinal chemistry.

[28]  S. Simon,et al.  Metalloproteinase Inhibitors, Nonantimicrobial Chemically Modified Tetracyclines, and Ilomastat Block Bacillus anthracis Lethal Factor Activity in Viable Cells , 2005, Infection and Immunity.

[29]  Sergey M Bezrukov,et al.  Blocking anthrax lethal toxin at the protective antigen channel by using structure-inspired drug design. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Dawoon Jung,et al.  Efficient synthetic inhibitors of anthrax lethal factor. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[31]  A. Steele,et al.  Anthrax lethal toxin induces endothelial barrier dysfunction. , 2005, The American journal of pathology.

[32]  E. Scolnick,et al.  Anthrax lethal factor inhibition , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[33]  S. Kaufmann,et al.  Human alpha-defensins neutralize anthrax lethal toxin and protect against its fatal consequences. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[35]  Milan Mrksich,et al.  Profiling kinase activities by using a peptide chip and mass spectrometry. , 2004, Angewandte Chemie.

[36]  M. Mrksich,et al.  Chemical screening by mass spectrometry to identify inhibitors of anthrax lethal factor , 2004, Nature Biotechnology.

[37]  Chi‐Huey Wong,et al.  Inhibition of the proteolytic activity of anthrax lethal factor by aminoglycosides. , 2004, Journal of the American Chemical Society.

[38]  M. Mock,et al.  Potent inhibitors of anthrax lethal factor from green tea , 2004, EMBO reports.

[39]  A. Bardwell,et al.  Anthrax lethal factor-cleavage products of MAPK (mitogen-activated protein kinase) kinases exhibit reduced binding to their cognate MAPKs. , 2004, The Biochemical journal.

[40]  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.

[41]  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.

[42]  S. Leppla,et al.  The roles of anthrax toxin in pathogenesis. , 2004, Current opinion in microbiology.

[43]  Ricardo M Biondi,et al.  Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. , 2003, The Biochemical journal.

[44]  E. Nishida,et al.  Molecular recognitions in the MAP kinase cascades. , 2003, Cellular signalling.

[45]  Xudong Liang,et al.  Anthrax Lethal Factor Proteolysis and Inactivation of MAPK Kinase* , 2003, The Journal of Biological Chemistry.

[46]  Ajay N. Jain.  Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. , 2003, Journal of medicinal chemistry.

[47]  M. Mrksich,et al.  Using mass spectrometry to characterize self-assembled monolayers presenting peptides, proteins, and carbohydrates. , 2002, Angewandte Chemie.

[48]  M. Mock,et al.  Pharmacology: Screening inhibitors of anthrax lethal factor , 2002, Nature.

[49]  Jerome Hauer,et al.  Anthrax as a biological weapon, 2002: updated recommendations for management. , 2002, JAMA.

[50]  M. Mrksich,et al.  Peptide chips for the quantitative evaluation of protein kinase activity , 2002, Nature Biotechnology.

[51]  Jadwiga Bienkowska,et al.  Crystal structure of the anthrax lethal factor , 2001, Nature.

[52]  B. Sellman,et al.  Dominant-Negative Mutants of a Toxin Subunit: An Approach to Therapy of Anthrax , 2001, Science.

[53]  M. Mock,et al.  Susceptibility of mitogen-activated protein kinase kinase family members to proteolysis by anthrax lethal factor. , 2000, The Biochemical journal.

[54]  A. Gearing,et al.  Design and therapeutic application of matrix metalloproteinase inhibitors. , 1999, Chemical reviews.

[55]  K D Paull,et al.  Proteolytic inactivation of MAP-kinase-kinase by anthrax lethal factor. , 1998, Science.

[56]  M. Hugh-jones,et al.  The Sverdlovsk anthrax outbreak of 1979. , 1994, Science.

[57]  M. Mock,et al.  Contribution of individual toxin components to virulence of Bacillus anthracis , 1991, Infection and immunity.

[58]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.

[59]  Lewis C Cantley,et al.  Identification of small molecule inhibitors of anthrax lethal factor , 2004, Nature Structural &Molecular Biology.

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