Molecular dynamics was used to simulate the transition state for the first chemical reaction step (TS1) of cocaine hydrolysis catalyzed by human butyrylcholinesterase (BChE) and its mutants. The simulated results demonstrate that the overall hydrogen bonding between the carbonyl oxygen of (؊)-cocaine benzoyl ester and the oxyanion hole of BChE in the TS1 structure for (؊)-cocaine hydrolysis catalyzed by A199S͞S287G͞A328W͞Y332G BChE should be significantly stronger than that in the TS1 structure for (؊)-cocaine hydrolysis catalyzed by the WT BChE and other simulated BChE mutants. Thus, the transition-state simulations predict that A199S͞ S287G͞A328W͞Y332G mutant of BChE should have a significantly lower energy barrier for the reaction process and, therefore, a significantly higher catalytic efficiency for (؊)-cocaine hydrolysis. The theoretical prediction has been confirmed by wet experimental tests showing an Ϸ(456 ؎ 41)-fold improved catalytic efficiency of A199S͞S287G͞A328W͞Y332G BChE against (؊)-cocaine. This is a unique study to design an enzyme mutant based on transitionstate simulation. The designed BChE mutant has the highest catalytic efficiency against cocaine of all of the reported BChE mutants, demonstrating that the unique design approach based on transition-state simulation is promising for rational enzyme redesign and drug discovery. molecular dynamics ͉ rational design ͉ transition-state stabilization ͉ cocaine ͉ enzyme-substrate binding C ocaine is recognized as the most reinforcing of all drugs of abuse (1-3). The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority (4-6). However, cocaine mediates its reinforcing and toxic effects by blocking neurotransmitter reuptake, and the classical pharmacodynamic approach has failed to yield small-molecule receptor antagonists because of the difficulties inherent in blocking a blocker (1-5). An alternative to receptor-based approaches is to interfere with the delivery of cocaine to its receptors or accelerate its metabolism in the body (5,(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). An ideal molecule for this purpose should be a potent enzyme catalyzing the hydrolysis of cocaine into biologically inactive metabolites. The dominant pathway for cocaine metabolism in primates is butyrylcholinesterase (BChE)-catalyzed hydrolysis at the benzoyl ester group (Fig. 3, which is published as supporting information on the PNAS web site), and the metabolites are all biologically inactive (5, 18). Clearly, BChE-catalyzed hydrolysis of cocaine at the benzoyl ester is the metabolic pathway most suitable for amplification. However, the catalytic activity of this plasma enzyme is Ϸ1,000-fold lower against the naturally occurring (Ϫ)-cocaine than that against the biologically inactive (ϩ)-cocaine enantiomer (19)(20)(21)(22). (ϩ)-cocaine can be cleared from plasma in seconds, before partitioning into the CNS, whereas (Ϫ)-cocaine has a plasma half-life of Ϸ45-90 min, long enough for ...

A novel computational protocol based on free energy perturbation (FEP) simulations on both the free enzyme and transition state structures has been developed and tested to predict the mutation-caused shift of the free energy change from the free enzyme to the rate-determining transition state for human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The calculated shift, denoted by ΔΔG(1→2), of such kind of free energy change determines the catalytic efficiency (k cat /K M ) change caused by the simulated mutation transforming enzyme 1 to enzyme 2. By using the FEP-based computational protocol, the ΔΔG(1→2) values for the mutations A328W/Y332A → A328W/Y332G and A328W/Y332G → A328W/Y332G/A199S were calculated to be -0.22 and -1.94 kcal/mol, respectively. The calculated ΔΔG(1→2) values predict that the change from the A328W/Y332A mutant to the A328W/Y332G mutant should slightly improve the catalytic efficiency and that the change from the A328W/Y332G mutant to the A328W/Y332G/A199S mutant should significantly improve the catalytic efficiency of the enzyme for the (-)-cocaine hydrolysis. The predicted catalytic efficiency increases are supported by the experimental data showing that k cat /K M = 8.5 × 10 6 , 1.4 × 10 7 , and 7.2 × 10 7 min -1 M -1 for the A328W/Y332A, A328W/Y332G, and A328W/Y332G/A199S mutants, respectively. The qualitative agreement between the computational and experimental data suggests that the FEP simulations may provide a promising protocol for rational design of highactivity mutants of an enzyme. The general computational strategy of the FEP simulation on a transition state can be used to study the effects of a mutation on the activation free energy for any enzymatic reaction.

The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.

Cocaine is recognized as the most reinforcing of all drugs of abuse. 1,2,3 There is no available anti-cocaine medication. The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority. 4,5,6 An ideal anti-cocaine medication would be to accelerate cocaine metabolism producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e. cocaine hydrolysis catalyzed by plasma enzyme butyrylcholinesterase (BChE). 5, 7 , 8 , 9 , 10 ,11 However, the native BChE has a low catalytic efficiency against naturally occurring (−)-cocaine.12 , 13 , 14 , 15 (−)-cocaine has a plasma half-life of ~ 45 -90 min, long enough for manifestation of the central nervous system (CNS) effects which peak in minutes. 13 , 16 Here we report an unconventional computational design leading to discovery of a human BChE mutant with a ~151-fold improved catalytic efficiency, which can be used as an exogenous enzyme in human to prevent (−)-cocaine from reaching CNS. The encouraging outcome not only provides a hopeful anti-cocaine medication, but also demonstrates that a novel general approach of studying enzymatic mechanism and computational drug design is promising.For rational design of a mutant enzyme with a higher catalytic activity for a given substrate, in general, one needs to design a mutation that can accelerate the rate-determining step of the entire catalytic reaction process while the other steps are not slowed down by the mutation. Reported computational modeling and experimental data indicated that the formation of the prereactive BChE-(−)-cocaine complex (ES) is the rate-determining step of (−)-cocaine hydrolysis catalyzed by wild-type BChE, 17, 18 , 19 , 20 , 21 , 22 ,23 whereas the rate-determining step for the faster hydrolysis of the biologically inactive (+)-cocaine enantiomer is the chemical reaction process consisting of four individual reaction steps (see Scheme 1).18 This mechanistic understanding is consistent with the experimental observation 17 that the catalytic rate constant of wild-type BChE against (+)-cocaine is pH-dependent, whereas that of the same enzyme against (−)-cocaine is independent of the pH. The pH-dependence of the rate constant for (+)-cocaine hydrolysis is clearly associated with the protonation of H438 residue in the NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript catalytic triad (S198, H438, and E325). For the first and third steps of the reaction process, when H438 is protonated, the catalytic triad cannot function and, therefore, the enzyme becomes inactive. The lower the pH of the reaction solution is, the higher the concentration of the protonated H438 is, and the lower the concentration of the active enzyme is. Hence, the rate constant was found to decrease with decreasing the pH of the reaction solution for the enzymatic hydrolysis of (+)-cocaine. 17 Based on the above mechanistic understanding, the previously reported efforts for ratio...

It is recognized that an ideal anti-cocaine treatment is to accelerate cocaine metabolism by producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e., butyrylcholinesterase (BChE)-catalyzed hydrolysis of cocaine. BChE mutants with a higher catalytic activity against (-)-cocaine are highly desired for use as an exogenous enzyme in humans. To develop a rational design for high-activity mutants, we carried out free-energy perturbation (FEP) simulations on various mutations of the transition-state structures in addition to the corresponding free-enzyme structures by using an extended FEP procedure. The FEP simulations on the mutations of both the free-enzyme and transition-state structures allowed us to calculate the mutation-caused shift of the free-energy change from the free enzyme (BChE) to the transition state, and thus to theoretically predict the mutation-caused shift of the catalytic efficiency (k(cat)/K(M)). The computational predictions are supported by the kinetic data obtained from the wet experiments, demonstrating that the FEP-based computational design approach is promising for rational design of high-activity mutants of an enzyme. One of the BChE mutants designed and discovered in this study has an approximately 1800-fold improved catalytic efficiency against (-)-cocaine compared to wild-type BChE. The high-activity mutant may be therapeutically valuable.