New Ultrahigh Affinity Host-Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

被引:289
作者
Moghaddam, Sarvin [3 ]
Yang, Cheng [1 ,2 ]
Rekharsky, Mikhail [1 ,2 ]
Ko, Young Ho [4 ,5 ]
Kim, Kimoon [4 ,5 ]
Inoue, Yoshihisa [1 ,2 ]
Gilson, Michael K. [3 ]
机构
[1] Osaka Univ, PRESTO JST, Suita, Osaka 5650871, Japan
[2] Osaka Univ, Dept Appl Chem, Suita, Osaka 5650871, Japan
[3] Univ Maryland, Inst Biotechnol, Ctr Adv Res Biotechnol, Rockville, MD 20850 USA
[4] Pohang Univ Sci & Technol, Natl Creat Res Initiat Ctr Smart Supramol, Dept Chem, Pohang 790784, South Korea
[5] Pohang Univ Sci & Technol, Div Adv Mat Sci, Pohang 790784, South Korea
基金
日本学术振兴会; 日本科学技术振兴机构;
关键词
PROTEIN-LIGAND; BINDING AFFINITIES; ENERGY; MOLECULES; HYDRATION; DYNAMICS; ENTROPY; DOCKING; CHARGES; SYSTEM;
D O I
10.1021/ja109904u
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A dicationic ferrocene derivative has previously been shown to bind cucurbit[7]uril (CB[7]) in water with ultrahigh affinity (Delta G degrees = -21 kcal/mol). Here, we describe new compounds that bind aqueous CB[7] equally well, validating our prior suggestion that they, too, would be ultrahigh affinity CB [7] guests. The present guests, which are based upon either a bicyclo[2.2.2] octane or adamantane core, have no metal atoms, so these results also confirm that the remarkably high affinities of the ferrocene-based guest need not be attributed to metal-specific interactions. Because we used the M2 method to compute the affinities of several of the new host-guest systems prior to synthesizing them, the present results also provide for the first blinded evaluation of this computational method. The blinded calculations agree reasonably well with experiment and successfully reproduce the observation that the new adamantane-based guests achieve extremely high affinities, despite the fact that they position a cationic substituent at only one electronegative portal of the CB[7] host. However, there are also significant deviations from experiment, and these lead to the correction of a procedural error and an instructive evaluation of the sensitivity of the calculations to physically reasonable variations in molecular energy parameters. The new experimental and computational results presented here bear on the physical mechanisms of molecular recognition, the accuracy of the M2 method, and the usefulness of host-guest systems as test-beds for computational methods.
引用
收藏
页码:3570 / 3581
页数:12
相关论文
共 34 条
[1]  
Ben-Naim A., 1992, STAT THERMODYNAMICS
[2]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[3]   Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm [J].
Chang, CE ;
Gilson, MK .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (40) :13156-13164
[4]   Tork: Conformational analysis method for molecules and complexes [J].
Chang, CE ;
Gilson, MK .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (16) :1987-1998
[5]   Calculation of molecular configuration integrals [J].
Chang, CE ;
Potter, MJ ;
Gilson, MK .
JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (04) :1048-1055
[6]   Ligand configurational entropy and protein binding [J].
Chang, Chia-en A. ;
Chen, Wei ;
Gilson, Michael K. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (05) :1534-1539
[7]   Concepts in receptor optimization: Targeting the RGD peptide [J].
Chen, W ;
Chang, CE ;
Gilson, MK .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (14) :4675-4684
[8]   Calculation of cyclodextrin binding affinities: Energy, entropy, and implications for drug design [J].
Chen, W ;
Chang, CE ;
Gilson, MK .
BIOPHYSICAL JOURNAL, 2004, 87 (05) :3035-3049
[9]   Identification of symmetries in molecules and complexes [J].
Chen, W ;
Huang, J ;
Gilson, MK .
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 2004, 44 (04) :1301-1313
[10]   Modeling Protein-Ligand Binding by Mining Minima [J].
Chen, Wei ;
Gilson, Michael K. ;
Webb, Simon P. ;
Potter, Michael J. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (11) :3540-3557