Download Reengineering Vancomycin

Reengineering Vancomycin to
Combat Bacterial Resistance
Matthew Giletto
September 18, 2013
CEM 958
Overview
• Why bacterial resistance to antibiotics is an
important area of research
• Review the history of vancomycin, its structural
elucidation and mechanism of action
• Track the development of bacterial resistance to
vancomycin
• Examine SAR work on vancomycin
• Learn how vancomycin has been assembled in
the laboratory and propose how this knowledge
may let us build ‘better’ vancomycin(s)
Bacterial resistance to antibiotics
• Meticillin resistant Staphylococcus aureus,‘MRSA’,
– killed 19,000 people (2005)
– invasively effected 94,000 in the US (2005)
– 3-4 billion dollars (2005)
• Vancomycin was ‘last line’ defense against multidrug
resistant pathogens
• Vancomycin resistant S. aureus, ‘VRSA’
• Vancomycin resistant Enterococci, ‘VRE’
• Resistance is acquired as a result of gene transfer from
nonpathogens to pathogens and between pathogens
Walsh, C. T.; Fischbach M. A. Sci. Am., 2009, 301, 44.
Klevens, R. M. et al. J. Am. Med. Assoc., 2007; 298, 1763.
Wengel, L. et. al. Science; 2003; 302 , 1569.
Neu, H.C. Science, 1992, 257, 1064.
Leclercq, R. et. al. N. Eng. J. Med., 1988, 319, 157.
Solution
• To use organic synthesis (total synthesis, semisynthesis and catalysis) as a tool to solve
problems in diverse areas of science
(chemistry, biology, medicine) that are not
solvable with other methods
Classes of antibiotics active against Gram
Positive pathogens
X-ray Structure of CDP-I
Bardsley, B., Williams, D. H.; Angew. Chemie. Int. Ed.; 1999; 38; 1172.
Williams, D. H.; Williamson, M. P.; J. Am. Chem. Soc.; 1981; 103; 6580.
Harris, C. M.; Harris, T. M.; J. Am. Chem. Soc.; 1982; 104; 4293.
Williams, D. H. et. al.; Nature; 1978; 271; 223.
Marshall, F. J.; J. Med. Chem.; 1965; 8; 18.
Rearrangement to CDP-I
Boger, D. L. et. al. J. Am. Chem. Soc., 1998, 120, 8920.
Harris, C. M.; Harris, T. M. J. Am. Chem. Soc., 1982, 104, 4293.
Key nOe’s of CDP-I and vancomycin
Nitanai, Y. et. al. J. Mol. Biol., 2009, 385, 1422.
Loll, P. J. J. Am. Chem. Soc., 1997, 119, 1516.
Williams, D. H.; Williamson, M. P.. J. Am. Chem. Soc., 1981, 103, 6580.
Vancomycin inhibits cell wall synthesis at
transglycosylation
• Schaefer: D-[1-13C]-ala incorporation exclusive to cell wall
precursors AND quantitatively detectable in solid state
NMR
• % D- [1-13C]-ala-D-[1-13C]-ala in growing Enterococci is 24
• % D- [1-13C]-ala-D-[1-13C]-ala 45 min after 25 mg/mL
vancomycin doubles to 48
– Diagnostic of accumulation of cell wall precursors in cytoplasm
Schaefer, J. et. al. Biochemistry, 2013, 52, 3405.
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1178.
Schaefer, J. et. al. J. Mol. Biol., 2006, 357, 1253.
Kricheldorf, H. R.; Muller, D. Macromolecules, 1983, 16, 615.
Bacterial cell wall synthesis: Phase 1
Schaefer, J. et. al. Biochemistry, 2013, 52, 3405.
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1253.
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Installation of D-asp bridge in Enterococci
Bellias, S. et. al. J. Biol. Chem., 2006, 281, 11586.
Phase 2
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Phase III Step 1:transglycosylation
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Binding model in susceptible bacteria
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Williams, D. H.; Bardsley, B. Angew. Chemie. Int. Ed., 1999, 38, 1172.
Williams, D. H. et. al. J. Am. Chem. Soc., 1983, 105, 1332.
Perkins, H.R.; Nieto, M. Biochem. J., 1971, 123, 789.
Binding model in resistant bacteria
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Williams, D. H.; Bardsley, B. Angew. Chemie. Int. Ed., 1999, 38, 1172.
Williams, D. H. et. al. J. Am. Chem. Soc., 1983, 105, 1332.
Perkins, H.R.; Nieto, M. Biochem. J., 1971, 123, 789.
Potential dual binding capacity of amidines
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Boger, D. L.; Crowley, B. M. J. Am. Chem. Soc., 2006, 128, 2885.
Activating the mechanism of resistance
Wright G. D. et. al. Nature Chemical Biology , 2010, 6, 327.
Probing the SAR for possible solutions to
bacterial resistance
Des-leucyl vancomycin series
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Kahne, D. et. al.; Science, 1999; 284, 507.
Williams, D H. et. al J. Antibiot., 1995, 48, 805.
Des-leucyl vancomycin series
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Kahne, D. et. al.; Science, 1999; 284, 507.
Williams, D H. et. al J. Antibiot., 1995, 48, 805.
Des-leucyl chlorobiphenyl vancomycin series
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1253.
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Kahne, D. et. al. Science, 1999, 284, 507.
Des-leucyl chlorobiphenyl vancomycin series
“The complexity of the peptide portion of
vancomycin makes it virtually impossible to
reengineer the peptide backbone to include
new contacts to the modified substrate.”
D. Kahne
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1253.
Kahne, D. et. al. Chem. Rev., 2005, 105, 425.
Kahne, D. et. al. Science, 1999, 284, 507.
Oritavancin
Zhanel, G. G. et. al. Drugs, 2010, 70, 859.
Schaefer, J. Biochemistry, 2008, 47, 10155.
Allen, N. et. al. J. Antibiot., 1997, 50, 677.
Oritavancin inhibits transpeptidation
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1253.
Site-Selective bromination of vancomycin
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Proposed Binding Model
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Modifications external to binding site
• Modifying carbohydrate = new mechanism
• Catalysis
Schaefer, J. et. al. Biochemistry, 2013, 52, 3405.
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Schaefer, J. et. al. J. Mol. Biol., 2009, 392, 1253.
Redesigning vancomycin
•
Total syntheses: Nicolaou, Evans, Boger
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Boger, D. L. et. al. J. Am. Chem. Soc., 1999, 121, 3226.
Smith, G. G. et. al. J. Org. Chem., 1983, 48, 5368.
Retrosynthetic analysis
Kahne, D. et. al. J. Am. Chem. Soc., 1998, 120, 11014.
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Boger, D. L. et. al. J. Am. Chem. Soc., 1999, 121, 3226.
Retrosynthesis of Eastern Hemisphere
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Boger, D. L. et. al. J. Am. Chem. Soc., 1999, 121, 3226.
Retrosynthesis of Western Hemisphere
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Boger, D. L. et. al. J. Am. Chem. Soc., 1999, 121, 3226.
The Nicolaou retrosynthetic approach
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Synthesizing the AB ring atropisomer
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Synthesizing the CD macrocycle
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Synthesizing the DE macrocycle
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Learning from the Nicolaou approach
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans’ Retro of the Western Hemisphere
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Synthesizing of AB macrocycle
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Synthesizing the CD macrocycle
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Preparing for the AB ring equilibration
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Equilibrating the AB macrocycle
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Evans, D. A. J. Am. Chem. Soc., 1993, 115, 6426.
Synthesizing the DE macrocycle
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Evans’ synthesis
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
Nicolaou versus Evans
Nicolaou, K. C. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2708.
Evans, D. A. et. al. Angew. Chemie. Int. Ed., 1998, 37, 2700.
The Boger strategy: Equilibration
Boger, D. L. et. al. J. Am. Chem. Soc., 1998, 120, 8920.
The Boger synthesis of vancomycin
amidine aglycon
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Incorporating the A ring
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Completion
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Vancomycin aglycon vs vancomycin
amidine aglycon
Boger, D. L.. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Dual binding capacity of amidines
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Analogs and factors influencing binding
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 8790.
An optimized analog: Amidine Oritavancin
Proposed traditional route
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Amidine Oritavancin
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Amidine Oritavancin
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Boger, D. L. et. al. J. Am. Chem. Soc.; 2012; 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Amidine Oritavancin
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Nicolaou, K. C. et. al. Chem. Eur. J., 1999, 5, 2648.
Amidine Oritavancin
Proposed peptide catalytic route to
Amidine Oritavancin
Boger, D. L. et. al. J. Am. Chem. Soc., 2012, 134, 1284.
Miller and Ley
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Ley, S. V. et. al. J. Chem. Soc. Perkin Trans. I, 2001, 358.
A combined approach
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Ley, S. V. et. al. J. Chem. Soc. Perkin Trans. I, 2001, 358.
A peptidomimetic Lawessons reagent
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Joullie, M. et. al. J. Am. Chem. Soc.; 2002; 124; 520.
Ley, S. V. et. al. J. Chem. Soc. Perkin Trans. I, 2001, 358.
Putative binding model
Miller, S.J.; Pathak, T.P. J. Am. Chem. Soc., 2012, 134, 6120.
Ley, S. V. et. al. J. Chem. Soc. Perkin Trans. I, 2001, 358.
Conclusions
• Important scientific problems can be better
understood and solved with the tools of
organic synthesis
• Specifically the problem of inevitable
evolution of bacterial resistance to antibiotics
can be countered in ways that only organic
synthesis could accomplish, restoring our
ability to combat deadly and otherwise
untreatable diseases
Thanks
• Dr. Tepe and current group members
– Nicole Hewlett
– Travis Bethel
– Greg Patten
– Jacob Ludwig
• Dr. Huang
• The audience
• Support of Holeigh, friends, and family