Daniel Kahne
Daniel Kahne, Ph.D.
Professor of Biological Chemistry and Molecular Pharmacology

The Kahne Lab is interested in the problem of antibiotic resistance. To develop new approaches to treat resistant bacterial infections, we focus on the protein machines that assemble the outer membrane that protects Gram-negative bacteria from toxic molecules.



For many years our research group has been interested in the molecular mechanisms of various antibiotics and the fundamental cellular processes they inhibit. We have primarily focused on drugs that target bacterial cell wall biosynthesis, including the beta-lactams, vancomycin, and moenomycin. We use these molecules to study the protein machines that synthesize and degrade the bacterial cell wall. Mechanistic studies of these classes of enzymes provide insight into the factors that determine bacterial cell shape, growth, and division. Recently, we have also become interested in understanding how the structure of cellular membranes is established and maintained. This is a stereochemical problem since biological membranes are asymmetric and require proper spatial organization of their constituent lipids and proteins in order to function correctly. We use E. coli as our model system and have identified two protein complexes that are involved in assembling lipids and proteins in the outer membrane of Gram-negative bacteria. Our challenge now is to determine how these machines function at a detailed chemical level and to explore their potential as antibacterial targets. A combination of sophisticated organic synthesis, bacterial genetics, biochemistry, and structural biology are required in these efforts.

In light of the public health threat posed by antibiotic resistance, current research in our laboratory is focused on essential processes in bacterial cell envelope biogenesis and on the antibiotics that target them. We seek to increase the fundamental understanding of these pathways and lay the groundwork for new antibacterial strategies. The following projects illustrate some of our current interests:

Bacterial Cell Wall Biosynthesis and Degradation: The cross-linked glycan polymer that surrounds bacterial cells dictates their cell shape and prevents them from lysing due to environmental changes in osmotic pressure. The peptidoglycan glycosyltransferases (PGTs) generate the cell wall, while the amidases, a group of hydrolases, degrade it in a controlled and coordinated manner during cell division. We are studying the mechanisms of these enzymes using chemically synthesized substrates (Lipid II and Lipid IV). We seek to identify the factors that determine bacterial cell shape, growth, and division. Because an intact cell wall is essential to bacterial cell survival, many commonly used antibiotics target enzymes in this pathway. Therefore, we are also studying how these antibiotics, including penicillin, cephalexin, vancomycin, and moenomycin, interact with their targets, alter cell wall synthesis, and induce cell death.

Inhibitory Mechanisms of Moenomycin A: The natural product moenomycin is the only known small molecule inhibitor of the peptidoglycan glycosyltransferases (PGTs). We are using this antibiotic as a tool to study the biochemical function of the PGTs and to determine the structural requirements for their inhibition. Moenomycin has superb in vitro activity but has not been used clinically because it possesses poor physical properties related to its phosphoglycerate lipid. We have developed a synthetic route to moenomycin A using the sulfoxide glycosylation method, which allows ready access to a variety of synthetic analogs. In collaboration with the Walker Lab at Harvard Medical School, we are using these analogs to probe the lipid chain length requirements, the role of the phosphate, the role of the glycerate, and the minimum number of sugar subunits required for transglycosylase inhibition and biological activity. In conjunction with structural studies of PGTs, these experiments will provide information about how PGTs can be inhibited and how moenomycin can be modified to make it more therapeutically useful.

Biogenesis of the Outer Membrane of Gram-negative Bacteria: The outer membrane is an important permeability barrier that consists of an asymmetric bilayer in which the inner leaflet is primarily composed of phospholipids and the outer leaflet is primarily composed of lipopolysaccharides (LPS). Outer membrane proteins (OMPs) of the β-barrel family span the bilayer and serve as channels and transporters. Using a chemical genetic approach, we recently identified two protein complexes in the outer membrane of Escherichia coli that are responsible for the assembly of OMPs and LPS. We are currently pursuing biochemical and structural studies of these complexes in order to understand how β-barrel proteins are folded and inserted into membranes and how the hydrophobic LPS molecule is transported to and assembled in the outer leaflet of the OM. We hope to identify whether there are general principles that guide the assembly of this membrane and to characterize these new protein targets for antibiotic development.


Naito Laboratory, Room 104

12 Oxford Street

Cambridge, MA 02138

Publications View
Robust Suppression of Lipopolysaccharide Deficiency in Acinetobacter baumannii by Growth in Minimal Medium.
Authors: Authors: Nagy E, Losick R, Kahne D.
J Bacteriol
View full abstract on Pubmed
Chemical tools to characterize peptidoglycan synthases.
Authors: Authors: Taguchi A, Kahne D, Walker S.
Curr Opin Chem Biol
View full abstract on Pubmed
Direction of Chain Growth and Substrate Preferences of Shape, Elongation, Division, and Sporulation-Family Peptidoglycan Glycosyltransferases.
Authors: Authors: Welsh MA, Schaefer K, Taguchi A, Kahne D, Walker S.
J Am Chem Soc
View full abstract on Pubmed
Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport.
Authors: Authors: Simpson BW, Pahil KS, Owens TW, Lundstedt EA, Davis RM, Kahne D, Ruiz N.
View full abstract on Pubmed
Fine-Tuning of sE Activation Suppresses Multiple Assembly-Defective Mutations in Escherichia coli.
Authors: Authors: Hart EM, O'Connell A, Tang K, Wzorek JS, Grabowicz M, Kahne D, Silhavy TJ.
J Bacteriol
View full abstract on Pubmed
FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein.
Authors: Authors: Taguchi A, Welsh MA, Marmont LS, Lee W, Sjodt M, Kruse AC, Kahne D, Bernhardt TG, Walker S.
Nat Microbiol
View full abstract on Pubmed
Structural basis of unidirectional export of lipopolysaccharide to the cell surface.
Authors: Authors: Owens TW, Taylor RJ, Pahil KS, Bertani BR, Ruiz N, Kruse AC, Kahne D.
View full abstract on Pubmed
Pathway-Directed Screen for Inhibitors of the Bacterial Cell Elongation Machinery.
Authors: Authors: Buss JA, Baidin V, Welsh MA, Flores-Kim J, Cho H, Wood BM, Uehara T, Walker S, Kahne D, Bernhardt TG.
Antimicrob Agents Chemother
View full abstract on Pubmed
Outer Membrane Translocon Communicates with Inner Membrane ATPase To Stop Lipopolysaccharide Transport.
Authors: Authors: Xie R, Taylor RJ, Kahne D.
J Am Chem Soc
View full abstract on Pubmed
A central role for PBP2 in the activation of peptidoglycan polymerization by the bacterial cell elongation machinery.
Authors: Authors: Rohs PDA, Buss J, Sim SI, Squyres GR, Srisuknimit V, Smith M, Cho H, Sjodt M, Kruse AC, Garner EC, Walker S, Kahne DE, Bernhardt TG.
PLoS Genet
View full abstract on Pubmed