By Sun Hongmao
This e-book won't be an exhaustive survey overlaying all points of rational drug layout. as an alternative, it will supply serious information via real-world examples. suitable case experiences might be awarded and analyzed to demonstrate the next: the best way to optimize a lead compound even if one has excessive or low degrees of structural details; tips on how to derive hits from rivals' energetic compounds or from typical ligands of the objectives; how one can springboard from rivals' SAR wisdom in lead optimization; tips to layout a ligand to intervene with protein-protein interactions through accurately studying the PPI interface; find out how to stay away from IP blockage utilizing info mining; the right way to build and entirely make the most of a knowledge-based molecular descriptor process; the right way to construct a competent QSAR version through targeting info caliber and correct number of molecular descriptors and statistical methods. a pragmatic consultant to Rational Drug layout makes a speciality of computational drug layout, with in basic terms uncomplicated assurance of biology and chemistry concerns, equivalent to assay layout, aim validation and artificial routes. Read more...
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Additional resources for A practical guide to rational drug design
7 Superposition of modeled 3-residue loop (magenta) in BACE1 with its crystal structure counterparts (Protein Data Bank ID: 1FKN, 2VNM, 4JOO). 6 Protonation of protein structures Hydrogen atoms are invisible in most crystal structures because of the insufficient crystal diffracting limit in X-ray crystallography. Discrimination of different heavy atoms and bond orders is also limited by data quality. Consequently, it is difficult to determine the rotamers of the –SH, –OH, and –NH3 groups in CYS, SER, THR, TYR, and LYS in crystal structures of proteins.
In such a situation, the problem is transformed into how to combine two molecules or fragments into one drug. 46 Besides matching the vectors in the query, the linkers that appear in the final hit list must meet the requirements specified in the filters and interact with the pocket residues without clashing with either the protein or the two fragments. The binding pocket and existing ligands are represented as exclusive volumes in MOE. The query was prepared by aligning the BACE1 crystal structure with the lead compound bound with another BACE1 structure whose ligand carried a cyclohexane moiety, such as structure 3MSK in the PDB.
Sanna, M. ; Han, G. ; Stevens, R. C. Science 2012, 335, 851. 7. Jaakola, V. ; Griffith, M. ; Hanson, M. ; Chien, E. ; Lane, J. ; Ijzerman, A. ; Stevens, R. C. Science 2008, 322, 1211. 8. Rasmussen, S. ; DeVree, B. ; Kruse, A. ; Chung, K. ; Kobilka, T. ; Thian, F. ; Chae, P. ; Mathiesen, J. ; Shah, S. ; Lyons, J. ; Gellman, S. ; Weis, W. ; Sunahara, R. ; Kobilka, B. K. Nature 2011, 477, 549. 9. ; Dore, A. ; Tehan, B. ; Mason, J. ; Marshall, F. H. Br J Pharmacol 2014, 171, 3132–3145. 10. ; Wang, M.
A practical guide to rational drug design by Sun Hongmao