Abstract
Interactions between a biological macromolecule and a small molecule ligand involve intricate recognition events which are strongly influenced by both structure and dynamics factors. The ligand and receptor must mutually fit and adapt to each other to form a strong complex, and detailed knowledge of these factors would certainly aid drug design efforts. This work describes our experience in the characterization and exploitation of these properties within the context of two medicinal chemistry programs that targeted the essential protease enzymes of the human cytomegalovirus (HCMV) and the hepatitis C virus (HCV). Central to the rational use of such data was the qualitative elucidation of the binding parameters that defined modes/roles of each substituent of the ligands. This required the development of dynamics- and structure-based strategies that logically considered data from structure–activity relationships, NMR spectroscopy, computational chemistry, and X-ray crystallography. An important emphasis was made to monitor the relationship between inhibitor activity and ligand flexibility using 13C NMR T 1 relaxation data, within the context of promoting the bioactive conformation as a drug design tool. Besides these methods which focused on data from the ligand perspective, interesting ligand-induced adaptive features of the receptors were also observed, and their impacts on drug design were explored.
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Abbreviations
- NMR:
-
nuclear magnetic resonance
- 13C T 1 :
-
13C NMR spin lattice relaxation
- IC50 :
-
inhibition constant at 50% concentration
- HCV:
-
hepatitis C virus
- HCMV:
-
human cytomegalovirus
- C-terminal:
-
C-terminus of a peptide chain
- N-terminal:
-
N-terminus of a peptide chain
- NOESY:
-
NMR nuclear Overhauser effect spectroscopy
- ROESY:
-
NMR rotating-frame nuclear Overhauser effect spectroscopy
- AIDS:
-
auto-immune deficiency syndrome
- HSV:
-
herpes simplex virus
- DLB:
-
NMR differential line broadening
- SAR:
-
structure-activity relationship
- NS:
-
non-structural
- HSQC:
-
NMR heteronuclear single-quantum correlation
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Acknowledgments
The work described herein involved many colleagues at Boehringer Ingelheim, and I would like to acknowledge their valuable contributions. I am also grateful to M. Bös, R. Bethell, and M. Cordingley for their encouragement and support. I also thank N. Aubry, S. Kawai, J. Gillard, P. White, and P. Bonneau for insightful discussions or for critical reading of the manuscript.
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LaPlante, S.R. (2006). Exploiting Ligand and Receptor Adaptability in Rational Drug Design Using Dynamics and Structure-Based Strategies. In: Peters, T. (eds) Bioactive Conformation I. Topics in Current Chemistry, vol 272. Springer, Berlin, Heidelberg . https://doi.org/10.1007/128_2006_087
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