Crystallography of membrane proteins, major targets in drug design

Structural biology approaches to antibacterial drug discovery

Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.

Immunoproteomic analysis and identification of novel immunogenic proteins from Vibrio harveyi

AIMS

The main aim of this study was to screen novel immunogenic proteins of Vibrio harveyi, which could be vaccine candidates.

METHODS AND RESULTS

  Whole-cell proteins of V. harveyi, strain Li01 and Huang01, were first separated by isoelectric focusing, followed by 2D-PAGE, respectively. Immunogenic proteins were identified by Western blotting, using Epinephelus coioides antisera against V. harveyi strain Li01. Western blot analyses revealed 16 shared immunogenic protein spots in both strains. All of the immunogenic proteins were successfully identified and corresponded to 15 proteins. None of these proteins have been previously reported as immunogenic for V. harveyi. Of the 15 proteins, 11 are specific immunoreactive proteins and four are nonspecific immunoreactive proteins. Furthermore, outer membrane protein N (spot 2) and oligopeptide ATP-binding cassette (ABC) transporter (spot 3) were used as immunogens to immunize E. coioides for investigation of their protective abilities and activities. The E. coioides immunized with OmpN has abilities to fight against infections caused by V. harveyi Li01 and Huang01. However, vaccination with oligopeptide ABC transporter induces low protective immune response in fish.

CONCLUSIONS

  Eleven novel specific antigens were found, and OmpN could potentially be used as vaccine candidate for the development of novel vaccine against V. harveyi.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data show that immunoproteomics methods can be successfully applied in identifying immunogenic proteins of V. harveyi, which helps to search for the protective antigens in future.

Recent applications of protein crystallography and structure-guided drug design

Technological advances to increase the throughput of purified protein production and co-crystallization of target proteins with small molecules have helped to solidify the role that structure via crystallography has on drug discovery. Visualization of how drug-like molecules bind to the target protein is a key step in driving follow-up or preclinical chemistry to improve characteristics of the molecule. Using structural information to guide small-molecule design and generate new chemical ideas is now a mainstay in the drug discovery process.

An association between ATP binding cassette systems, genome sizes and lifestyles of bacteria

Comparative bioinformatic analyses of ATP binding cassette (ABC) systems encoded in bacterial genomes have been undertaken in order to examine whether the range and distribution of these systems correlates with niches occupied by different organisms. In general, bacteria with larger genomes were found to encode more ABC systems than those with smaller genomes. Environmental bacteria, generally containing the largest genomes, showed the greatest number and diversity of ABC systems. Extracellular bacteria have larger genomes and show higher relative numbers of ABC transporters in comparison to intracellular bacteria. Similar results were obtained when comparing bacteria with different respiratory requirements since aerobic bacteria have larger genomes and also display greater numbers of ABC systems than anaerobes. These results suggest that the number of ABC systems encoded in bacterial genomes correlates with genome size and also with the physiological niche in which bacteria live. Furthermore, the distribution of the ABC systems into families indicates that the process of reductive evolution is responsible for retaining particular types of ABC systems as bacteria adapt to particular niches.