Prenyldiphosphate Synthase Inhibitors: Novel Anti-Infective Agents

Summary

Principal Investigator: Eric Oldfield
Affiliation: University of Illinois
Country: USA
Abstract: The broad, overall objective of this work is to develop novel anti-infective agents which target the isoprene biosynthesis pathways in protozoa and bacteria by using a combination of x-ray crystallography, NMR spectroscopy, calorimetry, enzyme and cell growth inhibition assays, QSAR (quantitative structure-activity relationship) techniques, quantum chemistry, synthesis, drug delivery and animal testing. The First Specific Aim is to use x-ray crystallography and solid-state NMR spectroscopy to investigate the structures of novel inhibitors bound to, primarily, farnesyl diphosphate synthase (FPPS) from Trypanosoma cruzi (the causative agent of American trypanosomiasis or Chagas disease), Trypanosoma brucei (the causative agent of African sleeping sickness), E. coli and Staphylococcus aureus, as well as human FPPS (the target for the bisphosphonate drugs used in treating bone resorption diseases, of interest in the context of designing inhibitor selectivity). Solid-state NMR will be used to complement the crystallographic results by providing dynamics (from 2H NMR) and protonation state information (from 13C, 15N, 31P chemical shifts) for use in the QSAR investigations. The Second Specific Aim is to investigate structure-function relationships. We will investigate inhibitor binding by using isothermal titration calorimetry and differential scanning calorimetry, as well as by using classical enzyme inhibition techniques, to deduce ligand binding constants (KB) and Kis together with thermodynamics of binding information for the systems studied in Aim 1. In addition, inhibitor binding to human bone and bone mineral models will be investigated using chromatographic and NMR techniques. These results will all then be analyzed by using QSAR methods, including the use of differential QSAR methods (to optimize parasite/bacterial inhibition versus human FPPS inhibition, and to minimize bone adsorption), together with the use of non-conventional QM descriptors and 2H NMR order parameters, to enhance the predictive utility of these methods. The Third and Final Specific Aim is to use the results from Aims 1 and 2 to design and then synthesize specific inhibitors of the isoprene biosynthesis pathway. These inhibitors will include novel pyridium, sulfonium and phosphonium species and will be designed to target unique polar residues found in the active site of the protozoal and bacterial enzymes. These inhibitors will then be formulated in bioavailable forms for use in animal testing. We will also focus on synergistic or combination therapy approaches by using two or three compounds, each of which target the isoprene biosynthesis pathway: such strongly synergistic interactions have already been observed and now need to be optimized using the novel inhibitors. Lay Summary: The research proposed is designed to lead to new therapeutic approaches to treat a variety of infectious diseases. In the US, these diseases are primarily bacterial and are a major public health threat while in the rest of the world, infectious diseases are mainly caused by protozoa. This work seeks to develop drugs to treat both sorts of disease.
Funding Period: 2002-06-01 - 2010-08-31
more information: NIH RePORT

Top Publications

  1. ncbi Pyridinium-1-yl bisphosphonates are potent inhibitors of farnesyl diphosphate synthase and bone resorption
    John M Sanders
    Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
    J Med Chem 48:2957-63. 2005
  2. ncbi The farnesyl-diphosphate/geranylgeranyl-diphosphate synthase of Toxoplasma gondii is a bifunctional enzyme and a molecular target of bisphosphonates
    Yan Ling
    Department of Pathobiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Biol Chem 282:30804-16. 2007
  3. ncbi NMR investigations of the static and dynamic structures of bisphosphonates on human bone: a molecular model
    Sujoy Mukherjee
    Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 130:1264-73. 2008
  4. ncbi A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence
    Chia I Liu
    Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan
    Science 319:1391-4. 2008
  5. ncbi Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases
    Rong Cao
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Proteins 73:431-9. 2008
  6. ncbi Bisphosphonate inhibitors of ATP-mediated HIV-1 reverse transcriptase catalyzed excision of chain-terminating 3'-azido, 3'-deoxythymidine: a QSAR investigation
    Yongcheng Song
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
    Bioorg Med Chem 16:8959-67. 2008
  7. ncbi Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
    Cammy K-M Chen
    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
    J Med Chem 51:5594-607. 2008
  8. ncbi Bisphosphonate inhibition of a Plasmodium farnesyl diphosphate synthase and a general method for predicting cell-based activity from enzyme data
    Dushyant Mukkamala
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 51:7827-33. 2008
  9. ncbi Phosphonosulfonates are potent, selective inhibitors of dehydrosqualene synthase and staphyloxanthin biosynthesis in Staphylococcus aureus
    Yongcheng Song
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 52:976-88. 2009
  10. ncbi Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation
    Yonghui Zhang
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:5153-62. 2009

Detail Information

Publications24

  1. ncbi Pyridinium-1-yl bisphosphonates are potent inhibitors of farnesyl diphosphate synthase and bone resorption
    John M Sanders
    Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
    J Med Chem 48:2957-63. 2005
    ..As such, they represent useful new leads for the discovery of new bone resorption, antiinfective and anticancer drugs...
  2. ncbi The farnesyl-diphosphate/geranylgeranyl-diphosphate synthase of Toxoplasma gondii is a bifunctional enzyme and a molecular target of bisphosphonates
    Yan Ling
    Department of Pathobiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Biol Chem 282:30804-16. 2007
    ....
  3. ncbi NMR investigations of the static and dynamic structures of bisphosphonates on human bone: a molecular model
    Sujoy Mukherjee
    Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 130:1264-73. 2008
    ....
  4. ncbi A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence
    Chia I Liu
    Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan
    Science 319:1391-4. 2008
    ..This finding represents proof of principle for a virulence factor-based therapy against S. aureus...
  5. ncbi Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases
    Rong Cao
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Proteins 73:431-9. 2008
    ..Overall, these results are of general interest since they show that some bisphosphonates can bind to more than one trans-prenyl synthase enzyme which, in some cases, can be expected to enhance their overall activity in vitro and in vivo...
  6. ncbi Bisphosphonate inhibitors of ATP-mediated HIV-1 reverse transcriptase catalyzed excision of chain-terminating 3'-azido, 3'-deoxythymidine: a QSAR investigation
    Yongcheng Song
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
    Bioorg Med Chem 16:8959-67. 2008
    ....
  7. ncbi Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
    Cammy K-M Chen
    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
    J Med Chem 51:5594-607. 2008
    ....
  8. ncbi Bisphosphonate inhibition of a Plasmodium farnesyl diphosphate synthase and a general method for predicting cell-based activity from enzyme data
    Dushyant Mukkamala
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 51:7827-33. 2008
    ..13). These results are of interest since they represent a general way to predict cell from enzyme inhibition data, with in three cases, R(2) values increasing from approximately 0.02 to 0.72...
  9. ncbi Phosphonosulfonates are potent, selective inhibitors of dehydrosqualene synthase and staphyloxanthin biosynthesis in Staphylococcus aureus
    Yongcheng Song
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 52:976-88. 2009
    ..These results open up the way to developing potent and selective inhibitors of an important virulence factor in S. aureus, a major human pathogen...
  10. ncbi Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation
    Yonghui Zhang
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:5153-62. 2009
    ....
  11. ncbi Inhibition of staphyloxanthin virulence factor biosynthesis in Staphylococcus aureus: in vitro, in vivo, and crystallographic results
    Yongcheng Song
    Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Med Chem 52:3869-80. 2009
    ..Given the good enzymatic, whole cell, and in vivo pharmacologic activities, these results should help guide the further development of novel antivirulence factor-based therapies for S. aureus infections...
  12. ncbi Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
    Rey Ting Guo
    Taiwan International Graduate Program, Institute of Biological Chemistry, Core Facility for Protein Crystallography, Academia Sinica, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 104:10022-7. 2007
    ....
  13. ncbi Bisphosphonates as inhibitors of Trypanosoma cruzi hexokinase: kinetic and metabolic studies
    Carlos E Sanz Rodríguez
    Laboratorio de Quimica Biologica, Centro de Biofisica y Bioquimica, Instituto Venezolano de Investigaciones Cientificas, Caracas 1020, Venezuela
    J Biol Chem 282:12377-87. 2007
    ..Taken together, our results suggest that these novel bisphosphonates act primarily as specific inhibitors of TcHK and may represent a novel class of selective anti-T. cruzi agents...
  14. ncbi Bisphosphonate inhibitors of Toxoplasma gondi growth: in vitro, QSAR, and in vivo investigations
    Yan Ling
    Laboratory of Molecular Parasitology, Department of Pathobiology and Center for Zoonoses Research, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, Urbana, Illinois, 61802, USA
    J Med Chem 48:3130-40. 2005
    ..Overall, these results indicate that alkyl bisphosphonates are promising compounds for further development as agents against Toxoplasma gondii growth, in vivo...
  15. ncbi Synthesis and biological evaluation of 1-amino-1,1-bisphosphonates derived from fatty acids against Trypanosoma cruzi targeting farnesyl pyrophosphate synthase
    Sergio H Szajnman
    , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, , Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
    Bioorg Med Chem Lett 15:4685-90. 2005
    ..cruzi farnesyl pyrophosphate synthase. As bisphosphonate-containing drugs are FDA-approved for the treatment of bone resorption disorders, their potential innocuousness makes them good candidates to control tropical diseases...
  16. ncbi Bisphosphonate inhibition of the exopolyphosphatase activity of the Trypanosoma brucei soluble vacuolar pyrophosphatase
    Evangelia Kotsikorou
    Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 48:6128-39. 2005
    ..brucei infection. The most active compound in vivo provided a 40% protection from death with no apparent side effects, suggesting that further development of such compounds may be of interest...
  17. ncbi Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: implications for drug design
    Sandra B Gabelli
    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    Proteins 62:80-8. 2006
    ....
  18. ncbi Inhibition of Trypanosoma cruzi hexokinase by bisphosphonates
    Michael P Hudock
    Department of Biophysics, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Med Chem 49:215-23. 2006
    ..2 microM IC(50) versus the clinically relevant intracellular amastigote form of T. cruzi, but only a approximately 1-2 mM IC(50) versus Dictyostelium discoideum and a human cell line, indicating selective activity versus T. cruzi...
  19. ncbi Design, synthesis, and biological evaluation of phosphinopeptides against Trypanosoma cruzi targeting trypanothione biosynthesis
    Esteban L Ravaschino
    , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, , Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
    J Med Chem 49:426-35. 2006
    ..The simple phosphinopeptide structure found as a pharmacophore in the present study constitutes a starting point for the development of straightforward optimized drugs...
  20. ncbi Amiodarone has intrinsic anti-Trypanosoma cruzi activity and acts synergistically with posaconazole
    Gustavo Benaim
    , , Apartado 21927, Caracas 1020A, Venezuela
    J Med Chem 49:892-9. 2006
    ..cruzi and open up the possibility of novel, combination therapy approaches to the treatment of Chagas' disease using currently approved drugs...
  21. ncbi Enthalpy versus entropy-driven binding of bisphosphonates to farnesyl diphosphate synthase
    Fenglin Yin
    Department of Biophysics, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Am Chem Soc 128:3524-5. 2006
    ....
  22. ncbi A solanesyl-diphosphate synthase localizes in glycosomes of Trypanosoma cruzi
    Marcela Ferella
    , , , Ministerio de Salud, Buenos Aires 1063, Argentina
    J Biol Chem 281:39339-48. 2006
    ..Because UQ has a central role in energy production and in reoxidation of reduction equivalents, TcSPPS is promising as a new chemotherapeutic target...
  23. ncbi Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes
    Junhong Mao
    Department of Chemistry and Biophysics, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Am Chem Soc 128:14485-97. 2006
    ....
  24. ncbi Thermodynamics of bisphosphonates binding to human bone: a two-site model
    Sujoy Mukherjee
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:8374-5. 2009
    ..95 (a 0.19 kcal error variance estimate, approximately 3% of the total DeltaG range), opening up the way to designing novel chemotherapy, immunotherapy, and anti-infectious disease drugs having weak bone binding affinity...