Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.
Here we apply the computational solvent mapping (CS-Map) algorithm toward the in silico identification of hot spots, that is, regions of protein binding sites that are major contributors to the binding energy and, hence, are prime targets in drug design. The CS-Map algorithm, developed for binding site characterization, moves small organic functional groups around the protein surface and determines their most energetically favorable binding positions. The utility of CS-Map algorithm toward the prediction of hot spot regions in druggable binding pockets is illustrated by three test systems: (1) renin aspartic protease, (2) a set of previously characterized druggable proteins, and (3) E. coli ketopantoate reductase. In each of the three studies, existing literature was used to verify our results. Based on our analyses, we conclude that the information provided by CS-Map can contribute substantially to the identification of hot spots, a necessary predecessor of fragment-based drug discovery efforts.
Landon
Melissa R
MR
Bioinformatics Graduate Program, Boston University, 24 Cummington Street, Boston, Massachusetts, USA.
Lancia
David R
DR
Yu
Jessamin
J
Thiel
Spencer C
SC
Vajda
Sandor
S
D000429:Alcohol Oxidoreductases / Q000737:chemistry; D000465:Algorithms; D000577:Amides / Q000737:chemistry; D001665:Binding Sites; D039301:Computers, Molecular; D015195:Drug Design; D029968:Escherichia coli Proteins / Q000737:chemistry; D005650:Fumarates / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012083:Renin / Q000737:chemistry; D013816:Thermodynamics
D000577:Amides; D029968:Escherichia coli Proteins; D005650:Fumarates; D011506:Proteins; C446481:aliskiren; D000429:Alcohol Oxidoreductases; C021934:2-dehydropantoate 2-reductase; D012083:Renin