. The glycopeptide antibiotics are the most important class of drugs used in the treatment of resistant bacterial infections, including methicillin-resistant S. aureus (MRSA). In fact, even after 60 years of clinical use, vancomycin administration in the clinic is still steadily increasing. Consequently, the emergence of resistant Gram-positive pathogens including vancomycin-resistant Enterococci (VRE) and vancomycin-resistant S. aureus (VRSA) presents a serious public health problem at a time few new antibiotics are being developed. These two pathogens rank 4th and 5th on the WHO global priority list of antibiotic-resistant bacteria for which there is an urgent need for new treatments. The only clinically significant mechanism of vancomycin resistance is its induced late stage remodeling of the bacterial cell wall precursor termini from D-Ala-D-Ala (the target of vancomycin) to D-Ala-D-Lac. Objectives of the work have included the redesign of vancomycin for dual D-Ala-D- Ala and D-Ala-D-Lac binding capable of treating both sensitive and vancomycin-resistant bacterial infections and directly addressing the underlying molecular basis of vancomycin resistance. The exciting results with binding pocket analogs designed for dual D-Ala-D-Ala/D-Lac binding and subsequently with their peripherally modified derivatives that incorporate synergistic second and third mechanisms of action (MOAs) independent of D-Ala-D- Ala/D-Lac binding chart a compelling path forward for the development of potent and especially durable antibiotics not prone to eliciting resistance for treatment of deadly vancomycin-resistant and multidrug-resistant bacterial infections. The studies in the last grant period have produced analogs worthy of comprehensive preclinical evaluation and the challenges for the work have returned to those of their preparation. This is an area where the PI and his group are well equipped and excited to address. The proposed studies will improve access to the analogs through development of an innovative next generation total synthesis or semisynthetic approach, and lay a foundation for fermentation access to the pocket modified glycopeptide antibiotics. The immediate target of the next generation synthetic studies, which are at an advanced stage, is the synthesis of an analog that is projected to be the most active compound in the series examined to date, bearing the most effective pocket modification and two key peripheral modifications. A well-conceived stereochemical simplification in the target structures will also be examined that will substantially improve synthetic access to the aglycon core structure without compromising antimicrobial activity. Optimization of activity derived from a new, third MOA discovered in the last grant period will be conducted and such efforts have already improved on the impressive activity reported to date. In vivo assessments of key compounds will be conducted that build on the stunning results to date, structural characterization of pocket analogs bound to model ligands will be pursued to confirm the fundamental basis of the remarkable dual D-Ala-D-Ala/D-Lac binding, and a breakthrough discovery for achieving antimicrobial activity against Gram-negative as well as Gram-positive bacteria will be examined.

Public Health Relevance

Fundamental new approaches and new therapeutics for the treatment of resistant bacterial infections (MRSA, VRSA, and VRE) will emerge from the studies, including the rational design of remarkably potent, broad spectrum, and especially durable antibiotics that possess multiple independent synergistic mechanisms of action acting on a common pathway. A fundamental understanding of the mechanism of action and the interaction of glycopeptide antibiotic natural products and their analogs with their biological targets will be defined.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Fu, Yali
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Wu, Zhi-Chen; Isley, Nicholas A; Boger, Dale L (2018) N-Terminus Alkylation of Vancomycin: Ligand Binding Affinity, Antimicrobial Activity, and Site-Specific Nature of Quaternary Trimethylammonium Salt Modification. ACS Infect Dis 4:1468-1474
Boger, Dale L (2017) The Difference a Single Atom Can Make: Synthesis and Design at the Chemistry-Biology Interface. J Org Chem 82:11961-11980
Okano, Akinori; Isley, Nicholas A; Boger, Dale L (2017) Peripheral modifications of [?[CH2NH]Tpg4]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics. Proc Natl Acad Sci U S A 114:E5052-E5061
Okano, Akinori; Isley, Nicholas A; Boger, Dale L (2017) Total Syntheses of Vancomycin-Related Glycopeptide Antibiotics and Key Analogues. Chem Rev 117:11952-11993
Okano, Akinori; Nakayama, Atsushi; Wu, Kejia et al. (2015) Total syntheses and initial evaluation of [?[C(?S)NH]Tpg?]vancomycin, [?[C(?NH)NH]Tpg?]vancomycin, [?[CH?NH]Tpg?]vancomycin, and their (4-chlorobiphenyl)methyl derivatives: synergistic binding pocket and peripheral modifications for the glycopeptide antib J Am Chem Soc 137:3693-704
Lee, Kiyoun; Poudel, Yam B; Glinkerman, Christopher M et al. (2015) Total synthesis of dihydrolysergic acid and dihydrolysergol: development of a divergent synthetic strategy applicable to rapid assembly of D-ring analogs. Tetrahedron 71:5897-5905
Hou, L; Jiang, J; Liu, B et al. (2014) Association between smoking and deaths due to colorectal malignant carcinoma: a national population-based case-control study in China. Br J Cancer 110:1351-8
Okano, Akinori; Nakayama, Atsushi; Schammel, Alex W et al. (2014) Total synthesis of [?[C(?NH)NH]Tpg(4)]vancomycin and its (4-chlorobiphenyl)methyl derivative: impact of peripheral modifications on vancomycin analogues redesigned for dual D-Ala-D-Ala and D-Ala-D-Lac binding. J Am Chem Soc 136:13522-5
Nakayama, Atsushi; Okano, Akinori; Feng, Yiqing et al. (2014) Enzymatic glycosylation of vancomycin aglycon: completion of a total synthesis of vancomycin and N- and C-terminus substituent effects of the aglycon substrate. Org Lett 16:3572-5
Pinchman, Joseph R; Boger, Dale L (2013) Probing the role of the vancomycin e-ring aryl chloride: selective divergent synthesis and evaluation of alternatively substituted E-ring analogues. J Med Chem 56:4116-24

Showing the most recent 10 out of 59 publications