Incorporating protein flexibility into docking and structure-based drug design

被引:25
作者
Barril, Xavier [1 ,2 ]
Fradera, Xavier [3 ]
机构
[1] ICREA, Barcelona 08028, Spain
[2] Univ Barcelona, Fac Farm, Dept Fis Quim, E-08028 Barcelona, Spain
[3] Organon Labs Ltd, Organon Res Scotland, Dept Med Chem, Newhouse ML1 5SH, Lancs, England
关键词
allostery; conformational flexibility; docking; induced-fit; structure-based drug design;
D O I
10.1517/17460441.1.4.335
中图分类号
R9 [药学];
学科分类号
1007 ;
摘要
The use of structure in drug design has become widespread, mainly thanks to recent advances in crystallography. Nevertheless, biological macromolecules are intrinsically flexible and it is increasingly evident that their function depends critically on both their structure and dynamics. In this review the authors discuss the implications of protein flexibility for drug design and review recent progress in incorporating protein flexibility into docking and structure-based drug design.
引用
收藏
页码:335 / 349
页数:15
相关论文
共 113 条
[1]   Receptor flexibility in de novo ligand design and docking [J].
Alberts, IL ;
Todorov, NP ;
Dean, PM .
JOURNAL OF MEDICINAL CHEMISTRY, 2005, 48 (21) :6585-6596
[2]   Crystal structure of an Hsp90-nucleotide-p23/Sba1 closed chaperone complex [J].
Ali, MMU ;
Roe, SM ;
Vaughan, CK ;
Meyer, P ;
Panaretou, B ;
Piper, PW ;
Prodromou, C ;
Pearl, LH .
NATURE, 2006, 440 (7087) :1013-1017
[3]  
Amadei A, 1999, PROTEINS, V35, P283, DOI 10.1002/(SICI)1097-0134(19990515)35:3<283::AID-PROT2>3.3.CO
[4]  
2-I
[5]   Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking [J].
Anderson, AC ;
O'Neil, RH ;
Surti, TS ;
Stroud, RM .
CHEMISTRY & BIOLOGY, 2001, 8 (05) :445-457
[6]   Conformation coupled enzyme catalysis: Single-molecule and transient kinetics investigation of dihydrofolate reductase [J].
Antikainen, NM ;
Smiley, RD ;
Benkovic, SJ ;
Hammes, GG .
BIOCHEMISTRY, 2005, 44 (51) :16835-16843
[7]  
Apostolakis J, 1998, J COMPUT CHEM, V19, P21, DOI 10.1002/(SICI)1096-987X(19980115)19:1<21::AID-JCC2>3.0.CO
[8]  
2-0
[9]   Direct determination of vibrational density of states change on ligand binding to a protein [J].
Balog, E ;
Becker, T ;
Oettl, M ;
Lechner, R ;
Daniel, R ;
Finney, J ;
Smith, JC .
PHYSICAL REVIEW LETTERS, 2004, 93 (02) :028103-1
[10]   Unveiling the full potential of flexible receptor docking using multiple crystallographic structures [J].
Barril, X ;
Morley, SD .
JOURNAL OF MEDICINAL CHEMISTRY, 2005, 48 (13) :4432-4443