Computational modeling of solvent effects on protein-ligand interactions using fully polarizable continuum model and rational drug design

Communications in Computational Physics

Volumn 13, Issue 1, 2013, Pages 31-60

  Zheng, Fang ^a   Zhan, Chang Guo ^a  

^a University of Kentucky   (United States)

Author keywords

Binding affinity; Protein ligand interaction; Rational drug design; Solvent effect

Indexed keywords

EID: 84866309680     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.130911.121011s     Document Type: Conference Paper

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117. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao,H.Nakai,M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L.Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, J. A. Pople, Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT, 2004.
118. C. J. Cramer and D. G. Truhlar, A universal approach to solvation modeling, Acc. Chem. Res., 41 (2008), 760-768.
119. J. Liu, C. P. Kelly, A. C. Goren, A. V. Marenich, C. J. Cramer, D. G. Truhlar, and C.-G. Zhan, Free energies of solvation with surface, volume, and local electrostatic effects and atomic surface tensions to represent the first solvation shell, J. Chem. Theory Comput., 6 (2010), 1109-1117.
120. C. P. Kelly, C. J. Cramer, and D. G. Truhlar, SM6: A density functional theory continuum solvation model for calculating aqueous solvation free energies of neutrals, ions, and solutewater clusters, J. Chem. Theory Comput., 1 (2005), 1133-1152.
121. D. Li, X. Huang, K. Han, and C.-G. Zhan, Catalytic mechanism of cytochrome P450 for 5'-hydroxylation of nicotine: Fundamental reaction pathways and stereoselectivity, J. Am. Chem. Soc. 133 (2011), 7416-7427.
122. J. Wu, Q. Liu, K. Yu, J. Hu, Y. P. Kuo, M. Seqerberg, P. A. St. John, and R. J. Lukas, Roles of nicotinic acetylcholine receptor beta subunits in function of human alpha4-containing nicotinic receptors, J. Physiol., 576 (2006), 103-118. (Pubitemid 44426224)
123. A. Karlin and G. G. Wilson, Acetylcholine receptor channelstructure in the resting, open, and desensitized states probed with thesubstituted-cysteine- accessibility method, Proc. Natl. Acad. Sci. U.S.A., 98 (2001), 1241-1248. (Pubitemid 32121217)
124. X. Cheng, H.Wang, B. Grant, S.M. Sine, and J. A.McCammon, Targetedmolecular dynamics study of C-loop closure and channel gating in nicotinic receptors, PLoS Comput. Biol., 2 (2006), 1173-1184. (Pubitemid 44495729)
125. X. Huang, F. Zheng, and C.-G. Zhan, Modeling differential binding of a4b2 nicotinic acetylcholine receptor with agonists and antagonists, J. Am. Chem. Soc. 130 (2008), 16691-16696.
126. Y. Pan, D. Gao, and C.-G. Zhan, Modeling the catalysis of anti-cocaine catalytic antibody: Competing reaction pathways and free energy barriers, J. Am. Chem. Soc., 130 (2008), 5140- 5149. (Pubitemid 351537074)
127. A. Hamza, X. Zhao, M. Tong, H.-H. Tai, and C.-G. Zhan, Novel human mPGES-1 inhibitors identified through structure-based virtual screening, Bioorg. Med. Chem., 19 (2011), 6077- 6086.
128. C.-G. Zhan, F. Zheng, and D. W. Landry, Fundamental reaction mechanism for cocaine hydrolysis in human butyrylcholinesterase, J. Am. Chem. Soc., 125 (2003), 2462-2474. (Pubitemid 36512233)
129. A. Hamza, H. Cho, H.-H. Tai, and C.-G. Zhan, Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants, J. Phys. Chem. B, 109(2005), 4776-4782. (Pubitemid 40429341)
130. D. Gao and C.-G. Zhan,Modeling effects of oxyanion hole on the ester hydrolysis catalyzed by human cholinesterases, J. Phys. Chem. B, 109 (2005), 23070-23076. (Pubitemid 43010734)
131. C.-G. Zhan and D. Gao, Catalyticmechanismand energy barriers for butyrylcholinesterasecatalyzed hydrolysis of cocaine, Biophys. J., 89 (2005), 3863-3872. (Pubitemid 41725608)
132. D. Gao and C.-G. Zhan, Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase, Proteins, 62 (2006), 99-110. (Pubitemid 43063008)
133. Y. Pan, D. Gao, W. Yang, H. Cho, G.-F. Yang, H.-H. Tai, and C.-G. Zhan, Computational redesign of human butyrylcholinesterase for anticocaine medication, Proc. Natl. Acad. Sci. USA, 102 (2005), 16656-16661. (Pubitemid 41688832)
134. D. Gao, H. Cho, W. Yang, Y. Pan, G.-F. Yang, H.-H. Tai, and C.-G. Zhan, Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation, Angew. Chem. Int. Ed., 45 (2006), 653-657. (Pubitemid 43121468)
135. Y. Pan, D. Gao,W. Yang, H. Cho, and C. G. Zhan, Free energy perturbation (FEP) simulation on the transition states of cocaine hydrolysis catalyzed by human butyrylcholinesterase and its mutants, J. Am. Chem. Soc., 129 (2007), 13537-13543. (Pubitemid 350071782)
136. F. Zheng,W. Yang,M.-C. Ko, J. Liu, H. Cho, D. Gao,M. Tong, H.-H. Tai, J.H.Woods, and C.- G. Zhan, Most efficient cocaine hydrolase designed by virtual screening of transition states, J. Am. Chem. Soc., 130 (2008), 12148-12155.
137. W. Yang, Y. Pan, L. Fang, D. Gao, F. Zheng, and C.-G. Zhan, Free energy perturbation simulation on transition states and high-activity mutants of human butyrylcholinesterase for (-)-cocaine hydrolysis, J. Phys. Chem. B, 114 (2010), 10889-10896.
138. W. Yang, Y. Pan, F. Zheng, H. Cho, H. H. Tai, and C.-G. Zhan, Free-energy perturbation simulation on transition states and redesign of butyrylcholinesterase, Biophys. J., 96 (2009), 1931-1938.
139. F. Zheng and C.-G. Zhan, Structure-and-mechanism-based design and discovery of therapeutics for cocaine overdose, Org. Biomol. Chem., 6 (2008), 836-843. (Pubitemid 351653352)
140. F. Zheng and C.-G. Zhan, Rational design of an enzyme mutant for anti-cocaine therapeutics, J. Computer-AidedMol. Design, 22 (2008), 661-671.
141. W. Yang, L. Xue, L. Fang, and C.-G. Zhan, Characterization of a high-activity mutant of human butyrylcholinesterase against (-)-cocaine, Chemico-Biological Interactions, 187 (2010), 148-152.
142. F. Zheng,W. Yang, L. Xue, S.Hou, J. Liu, and C.-G. Zhan, Design of high-activitymutants of human butyrylcholinesterase against (-)-cocaine: Structural and energetic factors affecting the catalytic efficiency, Biochemistry, 49 (2010), 9113-9119.
143. F. Zheng and C.-G. Zhan, Recent progress in protein drug design and discoverywith a focus on novel approaches to the development of anti-cocaine medications, Future Med. Chem. 1 (2009), 515-528.
144. F. Zheng and C.-G. Zhan, Enzyme therapy approaches for treatment of drug overdose and addiction, Future Med. Chem., 3 (2011), 9-13.
145. L. Xue, M.-C. Ko, M. Tong, W. Yang, S. Hou, F. Zheng, J. H. Woods, H. H. Tai, and C.-G. Zhan, Rational design, preparation and characterization of high-activity mutants of human butyrylcholinesterase against (-)-cocaine,Mol. Pharmacol., 79 (2011), 290-297.
146. Teva Pharmaceutical Industries Ltd, BChE Albumin Fusions for the Treatment of Cocaine Abuse, PCTWO 2011/071926 A1 (International Publication Date: June 16, 2011).
147. D. Gao, D. L. Narasimhan, J. Macdonald, M.-C. Ko, D. W. Landry, J. H. Woods, R. K. Sunahara, and C.-G. Zhan, Thermostable variants of cocaine esterase for long-time protection against cocaine toxicity, Mol. Pharmacol., 75 (2009), 318-323.
148. G. T. Collins, R. L. Brim, D. Narasimhan, M.-C. Ko, R. K. Sunahara, C.-G. Zhan, and J. H.Woods, Cocaine esterase prevents cocaine-induced toxicity and the ongoing intravenous self-administration of cocaine in rats, J. Pharm. Exp. Ther. 331 (2009), 445-455.
149. R. L. Brim,M. R.Nance, D.W. Youngstrom, D.Narasimhan, C.-G. Zhan, J. J. G. Tesmer, R. K. Sunahara, and J.H.Woods, A thermally stable formof bacterial cocaine esterase: A potential therapeutic agent for treatment of cocaine abuse, Mol. Pharmacol., 77 (2010), 593-600.
150. D. Narasimhan, M. R. Nance, D. Gao, M.-C. Ko, J. Macdonald, P. Tamburi, D. Yoon, D. M. Landry, J. H. Woods, C.-G. Zhan, J. J. G. Tesmer, and R. K. Sunahara, Structural analysis of thermostabilizing mutations of cocaine esterase, Protein Eng. Des. Sel. 23 (2010), 537-547.
151. C.-G. Zhan, Novel pharmacological approaches to treatment of drug overdose and addiction, Expert Rev. Clinical Pharmacology, 2 (2009), 1-4.