NMRand Drug Discovery

Abstract

In this chapter we give an overview of the two major approaches used in NMR and drug discovery: structure‐based design and NMR‐based screening. Combined with the more traditional uses of NMR in medicinal chemistry, they demonstrate the versatility of NMR as a tool for drug discovery. Structure‐based design is considered in two parts, ligand‐based design and receptor‐based design. In the former, NMR provides information on structure elucidation of drug leads, conformational analysis, charge state, tautomeric equilibria, and molecular dynamics and assists in the development of pharmacophore models. In receptor‐based design NMR allows the structures of macromolecular drug targets to be determined and their interactions with ligands to be elucidated. NMR‐based screening is a newer application of NMR technology in drug discovery but it is showing great promise as a tool for lead generation and optimization. Screening approaches based on chemical‐shift perturbation, magnetization transfer, diffusion, relaxation, NOEs, and spin labels are described. The utility of NMR has been enhanced over the last decade by developments in both instruments and methodology. On the instrumental side, increases in magnetic field strengths and the development of cryoprobes have increased sensitivity. Linkages of NMR to liquid chromatography and/or mass spectrometry have increased versatility. On the methods front there have been a range of new approaches discovered that will enhance the study of larger molecular complexes. Advances in protein expression and labeling have played a major role in stimulating the development of new NMR pulse sequences to extract information from such complexes.

Backbone Dynamics of Cyclotide MCoTI‐I Free and Complexed with Trypsin

“…Their unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal and enzymatic degradation (Scheme 1).Furthermore, their well-defined structures have been associated with a wide range of biological functions. [2,3] Cyclotides MCoTI-I/II are powerful trypsin inhibitors (K i % 20-30 pm) that have been recently isolated from the dormant seeds of Momordica cochinchinensis, a plant member of the cucurbitaceae family. [4] Although MCoTI cyclotides do not share significant sequence homology with other cyclotides beyond the presence of the three cystine bridges, structural analysis by NMR spectroscopy has shown that they adopt a similar backbone-cyclic cystine-knot topology.…”

“…S 2 values for residues 5 and 23 from free MCoTI-I are not included in the average because the relaxation data could not be fitted to a monoexponential function. [b] S 2 values for residues2,5,8,18,19,23,29,31,32, and 33 from trypsin-bound MCoTI-I are not included in the…”