Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.
The 1.8 A resolution de novo structure of nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) from Trypanosoma brucei (TbNDRT) has been determined by SADa phasing in an unliganded state and several ligand-bound states. This enzyme is important in the salvage pathway of nucleoside recycling. To identify novel lead compounds, we exploited "fragment cocktail soaks". Out of 304 compounds tried in 31 cocktails, four compounds could be identified crystallographically in the active site. In addition, we demonstrated that very short soaks of approximately 10 s are sufficient even for rather hydrophobic ligands to bind in the active site groove, which is promising for the application of similar soaking experiments to less robust crystals of other proteins.
Bosch
Jürgen
J
Department of Biochemistry, Division of Infectious Disease, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
Robien
Mark A
MA
Mehlin
Christopher
C
Boni
Erica
E
Riechers
Aaron
A
Buckner
Frederick S
FS
Van Voorhis
Wesley C
WC
Myler
Peter J
PJ
Worthey
Elizabeth A
EA
DeTitta
George
G
Luft
Joseph R
JR
Lauricella
Angela
A
Gulde
Stacey
S
Anderson
Lori A
LA
Kalyuzhniy
Oleksandr
O
Neely
Helen M
HM
Ross
Jenni
J
Earnest
Thomas N
TN
Soltis
Michael
M
Schoenfeld
Lori
L
Zucker
Frank
F
Merritt
Ethan A
EA
Fan
Erkang
E
Verlinde
Christophe L M J
CL
Hol
Wim G J
WG
D000595:Amino Acid Sequence; D000818:Animals; D001592:Benzyl Alcohols / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites; D018360:Crystallography, X-Ray; D007211:Indoles / Q000737:chemistry / Q000494:pharmacology; D007546:Isoquinolines / Q000737:chemistry / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010430:Pentosyltransferases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D011804:Quinolines / Q000737:chemistry / Q000494:pharmacology; D013329:Structure-Activity Relationship; D014344:Trypanocidal Agents / Q000737:chemistry* / Q000494:pharmacology; D014346:Trypanosoma brucei brucei / Q000187:drug effects / Q000201:enzymology*
D001592:Benzyl Alcohols; D007211:Indoles; D007546:Isoquinolines; D008024:Ligands; D011804:Quinolines; D014344:Trypanocidal Agents; D010430:Pentosyltransferases; C021888:nucleoside deoxyribosyltransferase