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, semi-synthesis 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

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.

“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

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