Many aspects of protein function, including molecular recognition, assembly and catalysis, depend on the 3D atomic structure. X-ray crystallography remains the most powerful method capable of providing atomic information on interactions of proteins with other macromolecules and small ligands. Third generation light sources and dedicated macromolecular crystallography (MX) beamlines have expanded our competence in determining protein structures. New strategies developed allow data collection from highly demanding crystals using mini-beams and reduce radiation damage. Genome sequencing projects have accelerated significantly and now include studies of many human pathogens. Expanded protein sequence space allows comprehensive approaches to studies of the entire cellular systems. Structural Genomics efforts took advantage of these innovations and contributed a complementary array of the rapid, highly integrated and cost effective methods in molecular and structural biology and created structure determination pipelines. When combined with MX synchrotron facilities, advanced software and computing resources, these pipelines resulted in significant acceleration of protein structure determination and expanded the range of projects.
Antibiotic resistance has been discovered against key antibiotics used in the treatment of many pathogenic strains that are found in various environments and poses a major threat worldwide. The continued evolution of a complex array of antibiotic-resistance genes presents a formidable challenge and efforts to develop new antimicrobials have lagged behind. Structure determination pipelines can be applied to emerging diseases and drug resistance. These studies can aid mechanistic analyses and structure-based drug discovery. The New Delhi Metallo-β-lactamase (NDM-1) gene makes multiple pathogenic bacteria resistant to all known β-lactam antibiotics. NDM-1 represents an example of extreme promiscuity - it is capable of efficiently hydrolyzing a wide range of β-lactams, including many "last resort" carbapenems; it can utilize different metal cofactors and seems to exploit alternative mechanisms. The structures of NDM-1 in complex with ligands revealed an enlarged and flexible active site capable of accommodating many β-lactam substrates. The zinc ions serve to activate a water molecule that hydrolyzes the β-lactam ring.
The development of new antibiotics that are effective against drug-resistant strains and the discovery of new drug targets are equally important. Recent progress on specific inosine-monophosphate dehydrogenase (IMPDH) inhibitors has prompted a new interest in bacterial IMPDHs as potential drug targets. IMPDH is considered a highly promising target because the protein controls the guanosine monophosphate pool and the gene is often found to be necessary for bacterial survival. Important differences between bacterial and eukaryotic enzymes can be utilized to design species-specific inhibitors. Structural studies of IMPDH in complex with different inhibitors combined with binding studies provide insight to how species-specific inhibitors can be developed.
This work was supported by NIH Grant GM094585, the NIAID/DHHS Contracts [HHSN272200700058C and HHSN272201200026C]. The use of SBC beamlines was supported by the U.S. DOE, BER [DE-AC02-06CH11357].