Alexei Savchenko

Savchenko laboratory pursues structure-function studies of microbial proteins involved in pathogenesis and conferring antibiotic resistance to provide the molecular framework for development of urgently needed novel antimicrobial therapies. In this research, we combine protein molecular structure visualization by X-ray crystallography and NMR spectrometry with biochemical and in vivo/infection studies.

Molecular basis of pathogen-host interactions
A wide range of Gram negative bacteria, including important plant, animal and human pathogens have evolved sophisticated secretion systems that allow bacteria to inject a specific set of proteins collectively called "effectors" inside their eukaryotic hosts. Once inside the host cell, effectors engage a diverse range of eukaryotic targets and systems to ensure successful infection and effectual immune system regulation. Unveiling the molecular function of bacterial effectors will greatly advance our understanding of pathogenesis and can lead to uncovering of novel eukaryotic cell biology pathways. However, this process is dampened by little to no sequence similarity between effectors and functionally characterised proteins, which does not allow confident prediction of effector function, leaving large portion of these proteins uncharacterized. We use 3D structure determination as segue into characterization of the function of variety effector proteins. This approach combined with biochemical and in vivo assays allowed us to unveil the function of several large families of effector proteins involved in hijacking of host ubiquitination system.

Clinical and emerging antibiotic resistance elements
Antibiotic resistance is a serious and growing health concern. Many clinically-relevant species, particularly so-called ESKAPE pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species evolve or acquire mechanisms rendering antibiotics ineffective.
In our lab, we are carrying out several structure-function and inhibition studies of proteins involved in clinically important and emerging antibiotic resistance mechanisms. Specifically, we pursue characterization of bacterial enzymes conferring resistance to the glycopeptide drug of last resort vancomycin, aminoglycosides, streptogramin compounds and other antibiotics. We use X-ray crystallography as our primary tool to produce detailed insights into molecular structure of these resistance elements and use this information to guide design of potent inhibitory scaffolds that can be used as antibiotic adjuvants for combined antimicrobial therapy.

Structural genomics
As one of founding members and active participants of international structural genomics effort our laboratory pursues the large-scale structural characterization of infection and antibiotic resistance related proteins from various bacteria of human and animal health relevance, including (but not restricted) Bacillus anthracis, Chlamydia trachomatis, Clostridium difficile, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Shigella flexneri, Staphylococcus aureus, Vibrio cholerae and Yersinia pestis. Using in-house developed methodologies and in collaboration with world renown microbial pathogenesis experts we operate a full protein structural characterization pipeline, including recombinant cloning, purification, crystallization and structure determination and interpretation. Obtained structural information is released to the unrestricted public use through the Protein Databank (PDB, www.rcsb.org/) to aid in research efforts dedicated to understanding the molecular basis of the infectious activity of these bacteria. Our laboratory is part of the Center for Structural Genomics of Infectious Diseases (CSGID, http://www.csgid.org/), which accepts nomination from microbiological community for protein targets for structural characterization.