Improving human health by enabling the development of drugs faster and cheaper is an important part of the NIH mission. This is partially achieved by introducing and constantly improving enabling technologies. 1 such technology is structure based drug design. Determining the structure of a small molecule (drug candidate or lead compound) to a biological receptor (protein implicated in disease) is a necessary step in this methodology. The dominant experimental approach used to achieve this goal is X-ray crystallography, while nuclear magnetic resonance (NMR) plays a lesser role in spite of large investments both in academia and industry. NMR is hampered by the size of protein that can be studied and the need to go through a lengthy structure determination process. However, NMR could play a greater role if it was possible to reduce the time effort necessary to solve the structure of a protein-ligand complex. Moreover, in cases where it is not possible to obtain a crystal NMR can play a significant role. Through the use of solid-state NMR studies, membrane proteins or proteins with solubility problems can be studied or in cases where only homology models of a protein are available NMR could play a role through the validation of active site structure hypotheses generated in homology modeling studies.
The aim of the proposed research is to extend and commercialize QuantumBio's successful linear-scaling semiempirical quantum mechanical NMR approach (NMRScore) to chemical shift perturbation (CSP) analysis. In Phase I of this proposal, the limits of applicability will be explored. In the Phase II proposal, extension of the methodology via reparameterization of 1H, 13C, 17O and 15N 1 13 17 15 NMR will be carried out. Furthermore, the streamlining of the workflow will be researched and implemented. Finally, this proposal is aiming to fully productize and commercialize this breakthrough technology. It is anticipated that by making this application commercially available the use of NMR in structure-based design efforts will be enhanced and the NMR tool and service market size can be further expanded. Significantly, the tool-box of structure based drug design will gain an important new method which will enable drug development for targets inaccessible to today's mainstream drug discovery paradigm. Thus, in the near future important underserved diseases can be targeted more efficiently. The successful completion of the Fast-Track STTR grant will have a major impact on improving human health. It will improve the quality of protein structures, facilitate the understanding of biomolecular dynamics and will provide higher quality structural insights into protein/ligand (drug) interactions which will enhance our ability to rationally design novel therapeutics for human diseases. ? ? ?
| Fu, Zheng; Li, Xue; Miao, Yipu et al. (2013) Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil. J Chem Theory Comput 9:1686-1693 |
| Wang, Bing; Westerhoff, Lance M; Merz Jr, Kenneth M (2007) A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem 50:5128-34 |
