Future Directions

Early stages of drug discovery continue to move further and further away from biofunctional screening assays such as bacterial broths, cell cultures, and animal models, and closer towards functional assays where specific (and targeted) inter

Fig. 10.8 SAR by MS applied to the A1061 construct (see text). (a) Structures of key motifs screened against the RNA target. Compound A is a D-amino acid. Compounds B1 and B2 are quinoxalin-2,3-diones. Compound AB is the rigid biaryl linked compound. (b) Binding affinity for the motifs when screened individually as well as binding affinity for motifs when screened in competition experiments are shown. Binding

Fig. 10.8 SAR by MS applied to the A1061 construct (see text). (a) Structures of key motifs screened against the RNA target. Compound A is a D-amino acid. Compounds B1 and B2 are quinoxalin-2,3-diones. Compound AB is the rigid biaryl linked compound. (b) Binding affinity for the motifs when screened individually as well as binding affinity for motifs when screened in competition experiments are shown. Binding is expressed as a normalized percent MS ion intensity of the RNA-ligand complex relative to the parent RNA such that a value of 100 indicates 50% of the ligand is bound to the target. A and B1 bind concurrently while A and B2 binding competitively. (c) MS determined Kd values for the RNA target and bacterial transcription/translation IC5o [T/T IC5o] values for selected structures.

actions are interrogated at the molecular level. It is not surprising that mass spectrometry continues to play an expanding role in this area as gas-phase measurements, which can be both highly automated and highly informative, can be used to interrogate macromolecular interactions of many different target/ligand classes.

The increasing availability of high performance mass spectrometry systems based on a number of different platforms (hybrid FTICRs, ESI-(Q)-TOFs, and novel traps such as the linear ion trap and orbitrap) should increase the implementation and utilization of existing ESI-MS-based methods, such as those outlined above, but should also catalyze the development of novel approaches to high throughput screening. Furthermore, preliminary studies with ion mobility measurements of macromolecular complexes [46] suggest that such measurements may provide invaluable information to drug discovery researchers as the combination of experimentally derived collisional cross-sections and computationally derived structure models hold great promise as rapid methods to interrogate modes of binding and allosteric interactions among drug targets and drug candidates. Several researchers have demonstrated that extremely large noncovalent complexes can be ionized and measured as intact species; complexes comprising the components of molecular machines such as megadalton protein complexes [47], self assembling ring structures [48], even intact ribosomes [49, 50] and viruses [51-53] have been successfully characterized by ESI-MS. It is quite likely that mass spectrometric analysis of these molecular machines and the small molecules with which they interact will be the ligand-substrate systems researchers employ to find the next generation of antibacterial and antiviral compounds. Might it be possible to discover new aminoglycosides by analyzing complexes formed between drug candidates and intact ribosomes? Might next-generation antiviral compounds be discovered by analyzing intact viruses in the presence of compounds that selectively disrupt the viral capsids or selectively bind to structural elements of the intact viral genome? While only time will tell just how far the mass spectrometric analysis of noncovalent complexes can push the envelope of modern drug discovery methods, it is clear that, at the rate the underlying analytical methods are evolving, the future of such methods has never looked better

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